Battling Rovers looked set to hang on for a credible point despite playing almost the entirety of the second half a man down after Tom Anderson was sent off for a late challenge on Matt Bloomfield.
But referee Michael Salisbury awarded a penalty to the hosts as he clocked ticked beyond the 90 minute mark after substitute Donervon Daniels collided with Adebayo Akinfenwa in the box.
Joe Jacobson slotted in the spot kick with confidence while Daniels limped off after being hurt in the penalty incident, leaving Rovers to play out eight minutes of added time with only nine men.
Rovers had struggled to get going when the numbers were even but did not look unduly troubled by a Wycombe side that had only lost once previously in the league this term.
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Darren Moore made one change to the side that beat AFC Wimbledon in the FA Cup in midweek with Rakish Bingham replacing Kwame Thomas.
It proved a slog of a first half from a Rovers perspective as sloppy possession play prevented them from mounting any considerable threat.
The hosts pressed very well in the middle of the park and Rovers struggled to get to grips with the approach, lacking their typical fluid play on the ball and conceding possession very cheaply.
There was a carelessness on the ball in their own half and an over-eagerness to find moment of magic in Wycombe's with both more often than not leading to the opposition regaining possession.
Rovers did have moments of early pressure with Anderson heading wide and swiping well over the bar, both from set pieces.
Wycombe soon began to take the initiative, with Alex Samuel striking wide before drawing a fine reaction save from Seny Dieng.
But neither side truly looked like scoring before the break.
Rovers’ task got all the more difficult four minutes into the second half.
Anderson lunged to meet a loose ball but caught Bloomfield high with his studs, bringing the inevitable red card.
Wycombe would understandably enjoy the better of the attacking play but struggled to really threaten as the Rovers defence held firm, with Daniels entering the fold to cover his colleague’s absence.
Daniels almost gave Rovers the lead with his first touch, looping a header onto the bar from a free kick.
And moments later Jon Taylor scuffed a shot at the keeper after excellent work from Reece James.
The visitors were then left feeding off scraps as Wycombe took control of possession.
Dieng produced a stunning save to tip wide from a flicked Samuel header.
The Rovers keeper had to be alert and was as a Jack Grimmer cross almost crept under the crossbar.
The decisive moment came as the game moved into added time.
Daniels charged in to meet a lofted ball into the box but smashed into Adebayo Akinfenwa, with referee Salisbury pointing straight to the spot.
Daniels was hurt in the incident and appeared to be forced off under the concussion protocol, leaving Rovers to play out the lengthy added time period with nine men.
Jacobson slotted in well to hand Wycombe the three points and take them five points clear at the top of the table.
With two of their centre halves set to miss some upcoming action, Rovers may well count the cost of this fixture.
WYCOMBE: Allsop; Grimmer, Stewart, Charles, Jacobson; Ofoborh, Bloomfield (Akinfenwa 60), Thompson; Wheeler, Samuel (Kashket 79), Smyth (Aarons 74). Subs not used: Yates, Gape, Phillips, Freeman.
ROVERS: Dieng; Halliday, Wright, Anderson, James (Sadlier 67); Sheaf, Whiteman; Taylor, Coppinger (May 80), Gomes (Daniels 54); Bingham. Subs not used: Lawlor, Amos, Greaves, Thomas.
REFEREE: Michael Salisbury (Lancashire)