Argyle’s win also all-but confirmed their place in the League Two end of season play-offs.
Plymouth’s 20-goal top scorer Reuben Reid fired Argyle into a seventh-minute 1-0 lead from the penalty spot.
The spot-kick was awarded after Max Power felled Dominic Blizzard as the midfielder broke into the area.
Power atoned for his foul by restoring parity with a thumping strike in the 34th minute.
However Tranmere’s joy was short-lived as on-loan Charlton wing-back Tareiq Dennis-Holmes scored his first goal for Plymouth.
Holmes-Dennis tackled Rory Donnelly as he broke from defence and barely took a stride before letting fly with a 30-yard screamer that gave diving Rovers keeper Owain Fon Williams little chance as it flew into the corner.
Jason Koumas came closest to levelling but his deflected 76th-minute shot, which looped over keeper Luke McCormick, was headed off the goal-line by Plymouth central defender Carl McHugh.
Argyle countered with substitute Zak Ansah teeing up Lewis Alessandra to make it 3-1 before Kayode Odejayi reduced the deficit in the 88th minute.