The under-par Terriers were outplayed for large periods in this match, played in from of a 15,000+ crowd, and looked like losing out after Rovers went ahead through Paul Rideout in the 24th minute.
Rideout was on the spot to volley home a Micky Mellon cross.
The veteran striker's goal was just the latest blow for the Terriers on what initially seemed to be a black day after Danny Schofield was ruled out of the matchday side with a thigh strain.
Town were already looking short of options with Adrian Moses not fit enough to start after picking up an injury in training - at least he was fit enough to take a place on the bench.
When Andy Booth succumbed to a knee injury after just 7 minutes it left the Terriers with a side which was desperately short of attacking options.
With Jason Koumas looking increasingly threatening during the match it was important that Town got their grip back on the game and Wijnhard set about the task with relish, making his physical presence known to Clint Hill - his marker - on several occasions.
Despite their efforts, however, Tranmere were on top for fully 70 minutes of the match. They were eager in the tackle, imaginative and generally first to the loose balls as Town struggled to match them in the blustery conditions.
Luck, however, was not on Tranmere's side.
Wayne Allison, on as a sub, missed a great chance to make it 2-0 for Tranmere and Town made them pay.
Craig Armstrong equalised in the middle of a goal mouth scramble. His final touch took a wicked deflection and wrong footed John Achterberg who had been impressive until then.
It took more than an equalising goal to get the home fans singing, though, and Chris Hay missed a chance laid on by Clyde Wijnhard before the Dutchman himself got onto the scoresheet a couple of minutes later.
Leon Knight was making waves down the right wing and he delivered a superb cross for Clyde Wijnhard to convert.
The Dutchman had positioned himself on the edge of the 6 yard box and headed home past Achterberg to rousing applause.
It was a fantastic comeback for the Terriers and they were rightly urged on by the crowd for a third.
Read Mel Booth's full match report in the Examiner on Monday. Have your say on the match in the message board below - selected comments may be published in the Examiner.
Town (4-4-2): Margetson, Jenkins, Gray, Evans, Clarke, Holland, Hay, Heary, Armstrong, Knight, Booth (Wijnhard 7)
Subs not used: P. Senior, Moses, Dyson, M. Senior
Booked: Knight, Evans, Jenkins
Scorers: Armstrong 75, Wijnhard 79
Tranmere (4-4-2): Achterberg, Yates, Roberts, Hill, Koumas, Barlow, Rideout (Allison 65), Flynn (Price 90), Sharps, Henry, Navarro (Mellon 19)
Subs not used: Murphy, Parkinson
Booked: Mellon, Barlow, Koumas
Scorer: Rideout 24
Referee: Phil Richards (Darwen)
Attendance: 15,784 (2,271)
See subsequent pages for match points
93 mins: Koumas lost his temper after a great tackle from Thomas Heary denied him a chance. He retaliated and committed a foul on Heary.
92 mins: Koumas' speculator was blocked as Tranmere piled on the pressure.
90 mins: Jason Price was brought on and he had 3 minutes of injury time in which to find and equaliser as the Terriers protected their lead.
90 mins: Barlow's right footed shot was blocked by Clarke.
88 mins: Knight showed great skill to turn and cross for Wijnhard.
87 mins: Hay was in the penalty area with Wijnhard looking for a 3rd goal but Tranmere hacked the ball away.
84 mins: Heary was taken out by a very late challenge by Mellon.
82 mins: Town were being backed by the Town crowd who had suddenly come to life. Gareth Evans was limping as the game pressed on.
80 mins: Hill cleared as Wijnhard hungrily chased his second of the match!
79 mins: A superb near post header saw Clyde Wijnhard open his Town account for the season after a wonderful delivery by Leon Knight. The Dutchman waited in the 6 yard box and struck!
77 mins: Chris Hay's shot was saved by Achterberg after Clyde Wijnhard led a counter-attack which almost capitalised on Rovers' mistake.
75 mins: Craig Armstrong's scrambled equaliser took a deflection and foxed Achterberg to level the scores after excellent work from Jenkins! Tranmere fans were still making all the noise though as the game was evenly poised.
73 mins: Big Chief Wayne Allison headed over the bar!
72 mins: Tranmere were winning the ball and keeping the pressure up on the Terriers.
71 mins: Knight left a foot in against Micky Mellon and there were ugly scenes as both sets of players got involved.
69 mins: Evans struck the ball over the bar after great work by Chris Holland sparked a scramble in the box.
67 mins: Armstrong's free kick found Knight but Achterberg was equal to Town's attack.
66 mins: Koumas rounded Evans but his shot was wide.
64 mins: Wayne Allison came on as Tranmere made changes to protect their lead.
61 mins: Paul Rideout appeared to attempt to headbutt Kevin Gray but the referee didn't do anything about it.
57 mins: Town were shaky as Tranmere won yet another free kick. Mellon took it and Barlow challenged Margetson for the ball.
52 mins: Town fans urged the Terriers on as, with the wind in their favour, they started to get some of the initiative back as at Swindon.
51 mins: Town won a corner after a ball into the box almost found Clarke.
50 mins: Koumas beat Clarke but the attack broke down when Rideout was deemed offside after Roves piled men forward to capitalise.
49 mins: Barlow got goalside of Clarke but Margetson was alert and picked up the loose ball.
48 mins: Thomas Heary struck a shot wide after great work by Clyde Wijnhard who held off a defender until he squared the ball.
47 mins: Holland cleared but lost control during a Tranmere attack.
Paul Rideout's right footed volley underlined a confident performance from Tranmere who led the Terriers 1-0 at half time.
Shorn of attacking options through Danny Schofield's pre-match injury and the loss of Andy Booth after just 7 minutes with a knee problem, the re-shuffled Terriers couldn't contain the Super Whites who set about harrassing them until they conceded the goal.
A better showing for Town towards the end of the first 45 minutes didn't hide the fact that the Terriers were badly missing Schofield, Booth and Moses.
47 mins: Hay carved out a chance for Holland to pull it back for Thomas Heary who shot wide!
46 mins: Koumas forced another diving save out of Margetson. He dived to his left to prevent Koumas' neat footwork and shot from putting the visitors 2-0 up.
45 mins: 4 added minutes were indicated as the Terriers slowly showed the fans that they were getting into the game with some close chances.
42 mins: Gray's flick at the near post found Armstrong in shooting mood but his drive was not on target.
38 mins: Gray's header at the near post was close after Armstrong's breathless run down the left flank produced a fine cross.
36 mins: Steve Jenkins was booked for a needless challenge.
35 mins: Koumas struck a free kick with vicious power and, with the wind behind him, was unlucky not to score as Margetson palmed it into the air and away.
34 mins: Tranmere were working hard as Town wasted what few opportunities came their way.
32 mins: Knight was flagged offside after Holland had won the ball and put the pass through.
31 mins: Jenkins' free kick came off Winjhard but fell to Clarke who blasted wide.
30 mins: Hill clattered Winjhard after a free kick was given.
29 mins: Rovers had dominated the play since the goal and were looking for for another goal.
28 mins: Clarke headed away a Tranmere free kick.
27 mins: CLyde Wijnhard was putting himself about after easing his way into the game and tussled with Clint Hill.
24 mins: Paul Rideout picked his spot and opened the scoring for Tranmere with a rasping volley.
20 mins: Barlow's strike came off the chest of Nathan Clarke and away for a corner.
18 mins: The game was starting to open up.
16 mins: Evans' late tackle saw Navarro on the ground in a heap.
14 mins: Clarke's long throw to the near post was cleared by Tranmere. The game was beginning to resemble a decent game as the opening scrappy moments were forgotten.
12 mins: The Terriers were getting little change out of the long ball game to Leon Knight. The Super Whites were flinging every single attempt to find the diminuitive Leon Knight back.
10 mins: A very flat game was producing little in the way of entertainment. The Terriers were clearly offering little in the way of attack without Booth and with such a defensive midfield on show.
7 mins: Clyde Wijnhard came on and was warmly greeted by Boothy as he limped heavily off.
5 mins: Knight's shot took a deflection and forced Achterberg to save with Hay lurking in the blustery conditions.
5 mins: It was disaster for Town as Andy Booth signalled to be substituted - Clyde Wijnhard was ready for a long stint in the game.
4 mins: Andy Booth bravely decided to play on and the game continued.
2 mins: Andy Booth took a knock to his knee early on and required lengthy treatment after landing awkwardly following a header.
An impeccably observed minutes silence preceded the kick off.
Danny Schofield picked up a back strain and was replaced by Thomas Heary. Adrian Moses was injured in training but was fit enough to make it onto the bench for the Terriers. Kevin Gray replaced the unlucky defender.
Tranmere arrived at the McAlpine with just one change - Stuart Barlow replaced Jason Price in attack while Jason Koumas was fit to take his place in the side.