The early signs had pointed toward a stalemate as there was little on target in the first half.
Danny Schofield's 20th minute curler curled wide.
Gareth Roberts put in a 25th minute cross which beat Steve Jenkins and fell to Paul Rideout.
The veteran striker found plenty of space for a good header but he could have done much better with his effort which didn't trouble Martyn Margetson's goal.
Nathan Clarke had had Town's best effort of the half from a Thorrington corner while John Thorrington himself had spurned a couple of chances to release the ball early to players who had found space in prime attacking positions.
Town started the second half hungry for a goal and Andy Booth, who had been given half chances in the first half, glanced a Steve Jenkins cross wide in the opening seconds.
Booth had a flicked header caught by Joe Murphy after another Town move but Nick Henry produced the shock goal from a Tranmere counter-attack.
Chris Holland had initially lost the ball and Thomas Heary slipped up trying to win it back which allowed Rovers to close in on Margetson and the final pass found Nick Henry on the edge of the 6 yard box and his turn and shot beat the Welshman.
The disappointment was clear but the Terriers pressed on and almost produced the equaliser when Thorrington's superbly hit corner flew into the area at the right height for a diving Andy Booth to head home from 6 yards out but he somehow headed the ball over the bar after beating all the Rovers defenders!
Lou Macari made tactical changes, bringing Chris Hay on for Adrian Moses with just over 20 minutes to go, but nothing seemed to go right for the Terriers and Rovers held on for their victory.
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Tranmere Rovers (4-4-2): Murphy, Yates, Roberts, Allen, Mellon, Koumas (Parkinson 64 (Hume 75)), Barlow, Rideout (Allison 79), Flynn, Sharps, Henry
Subs not used: Challinor, Achterberg
Booked: Yates, Roberts
Scorer: Henry 50
Town (4-4-2): Margetson, Heary, Moses (Hay 69), Gray, Clarke, Jenkins, Thorrington, Mattis, Holland, Booth, Schofield
Subs not used: P. Senior, Dyson, Macari, Brown
Referee:Mark Clattenburg (Chester-le-Street)
See subsequent pages for match points.
93 mins: Andy Booth's knock down fell to Wayne Allison who belted the ball upfield as the referee blew for full time.
92 mins: Andy Booth was deemed to be at fault after he was sandwhiched between two defenders.
91 mins: 3 minutes of extra time were added while Andy Booth missed another header.
90 mins: Thorrington was pulled down by Roberts after a surging run to the penalty area.
89 mins: Chris Holland forced Joe Murphy into a great low save on his right.
87 mins: Hume inexplicably put the ball out of play during a Tranmere attack.
84 mins: Wayne Allison went down under a great challenge in the Town box by Kevin Gray but the big man still managed to get the ball to a Rovers team-mate.
82 mins: Nathan Clarke's big throw was cleared by Wayne Allison.
80 mins: Town won a free kick but Thorrington's set piece was deflected behind for a corner.
79 mins: Wayne Allison, on as a sub, went up for a header with Kevin Gray and knocked his former Town team-mate down.
75 mins: Nathan Clarke timed his tackle well to keep Hume out of goal contention.
70 mins: Andy Booth headed over the bar again from the corner.
69 mins: John Thorrington won a corner after he was put through by Chris Holland.
68 mins: Chris Hay replaced Adrian Moses as Lou Macari switched Thomas Heary to right back and slotted Hay into midfield.
66 mins: Chris Hay was ready to come on as Town continued to chase the equaliser.
64 mins: Gray seemed to be shoved by Stuart Barlow as he tried to get under the ball which he allowed to bounce.
62 mins: Andy Parkinson replaced Jason Koumas.
58 mins: Thorrington's great corner was begging to be turned into the Tranmere goal but it was somehow headed over the bar by an unmarked Andy Booth!!
56 mins: Koumas drove downfield but was driven wide by the flight of the ball he was chasing and Steve Jenkins.
54 mins: Town pressurised the Rovers defence and claims for a shirt pull in the area were ignored before Nathan Clarke glanced a header from Holland's knockdown just wide of the mark.
49 mins: Town quickly responded and Danny Schofield couldn't get enough of a deflection on a cross to divert it past Murphy.
48 mins: Nick Henry volleyed from 6 yards out to open the scoring for Tranmere. He finished off a lightning counter-attack after Chris Holland lost the ball and Thomas Heary slipped up trying to win it back in midfield.
47 mins: Booth's flicked header was caught by Murphy after Schofield had set Thorrington off on a run.
47 mins: Danny Schofield was adjudged offside after he started his run too early for Heary's pass.
46 mins: A quick start by Town saw Steve Jenkins finish off a flowing attack with a cross which Andy Booth glanced wide.
HALF TIME: Town were well marshalled in a fairly workmanlike first half but they lacked adventure. John Thorrington spurned a couple of chances to release the ball early to players who who were unmarked and in space. Nathan Clarke had Town's best effort in the first half from a Thorrington corner but this was a forgettable 45 minutes.
46 mins: Flynn was harried all the way back to Margetson's area by Thomas Heary where the Welsh goalkeeper took over and collected the ball.
45 mins: 2 minutes of added time were indicated.
44 mins: Koumas' attempted scissors kick was cleared in a panic as a flurry of action happened in the closing stages of the half. A great header by Nathan Clarke tested Murphy while John Thorrington failed to see Danny Schofield in plenty of space before he was tripped on a good run.
42 mins: Town were unadventurous as Tranmere increasingly defended deep themelves.
35 mins: Nathan Clarke's long throw went past Andy Booth straight through to Joe Murphy.
33 mins: A typical Tranmere set piece saw Andy Booth and Steve Jenkins combine to clear the threat.
32 mins: Koumas put in a great cross which Margetson came to catch under pressure from the oncoming Tranmere strikers.
30 mins: Barlow tried to chip the ball to Mickey Mellon but the ball was cleared. Tranmere had pushed on in numbers looking the opener but Town procrastinated.
26 mins: Yates scrambled clear from a Town set piece after Booth's flick-on caused panic in the home defence.
25 mins: Roberts' fine delivery foxed Jenkins and found Rideout but the veteran striker found the space to get a good header in which didn't trouble Margetson - the only real chance for either side so far. The Terriers were defending deep though, with two deep defenders looking out for probing runs from the Rovers wide men.
20 mins: Schofield's attempted curler flew well wide in a generally quiet start to the half.
15 mins: Booth rose for a header but, under pressure, his effort was off target.
10 mins: Joe Murphy cleared as John Thorrington raced Graham Allen to get to a through ball.
6 mins: Mattis released Thorrington for a great run and cross which Town's attackers misread and Murphy came to collect.
5 mins: Flynn cleared as Town gathered in the Tranmere area.
3 mins: Mattis skied a chance with team-mates waiting for a lay-off.
Adrian Moses made a rare start in place of Kenny Irons who failed a fitness test on his groin injury from Thursday. With Thomas Heary moving to midfield, Moses seemed set to start in defence.
Long term injury victim Jon Dyson returned to the Town squad for the first time since April and his was joined on the bench by Nat Brown, a promising youth team striker.