ANDY BOOTH claimed a close-range winner with his 175th career goal as Town took all three points without ever really getting into top gear.
A combination of enforced changes plus a hangover from the derby win over Leeds meant Tranmere were able to boss the first half.
But Town started the second better and were strong enough to see off a Birkenhead side who beat them 3-0 at Prenton Park back in October.
Keeper Matt Glennon can boast three successive clean sheets for only the second time in a Town shirt.
And striker Booth now has 141 goals for the club (eight this season) to go with his 34 for Sheffield Wednesday after being in the right place at the right time in the 61st minute.
Midfielder Michael Collins, who rapped the bar against Leeds, did all the hard work after playing a neat one-two with Joe Skarz.
He sliced through the home defence and looked set to score a deserved goal until Welsh international keeper Danny Coyne stretched to parry.
The ball fell right into the path of Booth, however, and the 34-year-old made no mistake.
Town had only one real scare thereafter, when Glennon missed former Middlesbrough man Robbie Stockdale’s 72nd-minute cross but was helped out by his defence.
Tranmere survived a couple, with Coyne smothering after Andy Holdsworth’s 73rd-minure corner led to a six-yard box scramble, then using his legs to deny Danny Schofield as the substitute burst through on goal after neat play by Holdsworth and Collins.
Then, in stoppage time, Schofield’s fellow bench man Luke Beckett picked out Collins in space as Town counter-attacked, but the 21-year-old was unable to get the ball under control, allowing the visitors to mop up the threat.
Tranmere had posed much of the danger in the first half, with Town taking time to settle.
Already forced to replace injured striker Chris Brandon and suspended midfielder Jon Worthington, caretaker manager Gerry Murphy lost holding midfielder James Berrett pre-match when he woke feeling pain in a knee after jarring the joint during training on Friday.
Murphy’s response was to keep faith with 3-5-2 by switching Holdsworth to midfield alongside Collins, playing Tom Clarke at right-back and Skarz in the holding role.
Malvin Kamara took Brandon’s frontline slot alongside Booth.
Kamara couldn’t quite make contact with an inviting flick-on by Booth as Nathan Clarke hurled in an 18th-minute long throw.
And Nathan Clarke headed across the face of goal from Holdsworth’s delivery seven minutes later.
But it was Tranmere, with former Town loan man Andy Taylor busy at left-back and ex-Barnsley player Chris Shuker lively on the right wing, who created the clearer opportunities for a first-half breakthrough.
Centre-back Ben Chorley looked on as his well-struck 15th-minute shot from Ian Moore’s nod down was blocked.
Then Moore, the son of Tranmere boss Ronnie and a Town target last close-season, was involved in a sweeping 32nd-minute move which ended with Glennon making a great save to thwart Shuker.
Taylor, who joined Tranmere from Blackburn during the January transfer window, was in space when he received Shuker’s 35th-minute pass, but Skarz was on hand to block a low shot.
Then, in the 40th minute, Glennon gathered Moore’s nod-on under pressure from Chris Greenacre.
Glennon’s last act of the opening period was to collect a speculative long-range effort by midfielder Steve Jennings, and the stopper, who has turned down a new-contract offer, had less to do in the second half.
This time if was Coyne who was called into action as Booth met Nathan Clarke’s 48th-minute long throw with an angled header.
Then Holdsworth’s clever delayed pass gave Schofield, on as a 52nd-minute replacement for Kamara, a chance, but big Jamaican defender Ian Goodison was quickly in to block.
Coyne held Robbie Williams’ right-foot shot on the turn in the 60th minute, but he was soon to be picking the ball from the back of the net as his side’s last hopes of a play-off challenge were extinguished.
Coyne, Stockdale, Goodison, Kay, Taylor, Shuker, Jennings, Chorley, Sherriff (Mullin, 76mins), Moore (Curran, 76mins), Greenacre.
Subs not used: Jones, Gornell, Achterberg.
Just one scary moment as he made it three straight clean sheets for only the second time as Town keeper.
Handed his first Town start since October 2006 at right-back and responded with a very solid show.
Stuck to his task against a tricky opponent in Chris Shuker and came close with a right-foot effort.
Once again very steady on the left of Town’s three-strong central defensive line.
Never shirked a challenge and while a few passes went astray, played a key part in the clean sheet.
Town’s latest skipper has been a model of consistency since arriving at the club. Let’s hope he stays!
Not that familiar with the holding midfield role and took time to settle, but made plenty of telling touches.
Showed his versatility by slotting seamlessly into a midfield berth for the first time under Gerry Murphy.
Followed up his fine display against Leeds with another bright performance. His attacking made Town’s goal.
Has had better games, but still popped up to produce his 141st goal in Town colours.
Worked hard at both ends of the pitch, but unable to make a real impact up front and came off in the 52nd minute.
Danny Schofield for Kamara, 52mins; Luke Beckett for Booth, 81mins. Not used: Aaron Hardy, Spencer Harris, Alex Smithies.Booked: Nathan Clarke.
West Midlands whistler Steve Bratt showed plenty of flexibility and common sense to keep the game flowing as much as possible.
Perhaps the warning given to Nathan Clarke for a first-half challenge on Ian Moore wasn’t merited, and that might well have contributed to the Town defender being shown a yellow card for his 75th-minute foul on Chris Shuker. But no other complaints!