An injury time goal brought Tranmere a twelfth home success and kept alive their play-off hopes.
But it was rough justice on a Wycombe side that adapted well after conceding a dozen goals in their previous three outings.
Wanderers continually frustrated Tranmere who were lacklustre for much of the 90 minutes.
But in the third minute of injury substitute Micky Mellon floated a free-kick in to the box and Gary Jones headed in to the top right hand corner for his seventh goal of the season.
Earlier Frank Talia in the Wanderers goal had denied the home side with several good saves including efforts from Simon Haworth and Iain Hume.
And the frustration increased for Tranmere when penalty appeals were turned down in the 66th minute when Hume and Tyrone Loran appeared to be floored in the box.
Wycombe themselves were not without their chances a Keith Ryan header in the 31st minute was tipped over by keeper Russell Howarth who saved with an out stretched leg from Johnny Dixon in the 59th minute.
Tranmere boss Ray Mathias said: "At the end of the day we have got to be pleased with the win but to be fair it was not what we deserved.
"We were not very good at all in the first half but the lads showed character and kept going and it worked out for us in the end." Wycombe boss Lawrie Sanchez was gutted, commenting: "We must have upset the footballing gods. We produced a good solid performance and it was so cruel to concede a goal so late. But we did not defend a free kick well enough and they have taken the points."