Lowe headed home with 14 minutes remaining after Jake Cassidy had flung in a perfect cross from the right.
Both sides scored a goal apiece during a first half which Oldham dominated.
The visitors went in front after 12 minutes when Australian midfielder James Wesolowski thumped home his fourth goal of the season from 18 yards following a neat one-two with Gary Harkins.
Harkins almost doubled the lead while Danny Philliskirk also went close before Rovers bagged a fortunate equaliser on the half-hour mark.
Lowe teed up Jason Koumas and his low driven shot from the edge of the penalty area struck Jonathan Grounds' foot and looped over unlucky Oldham goalkeeper Mark Oxley.
The visitors restored their lead with their own lucky strike after 59 minutes. This time David Worrall crossed in low and when the ball was not cleared it struck the shin of Tranmere defender Liam Ridehalgh before trickling past 'keeper Owain Fon Williams.
However, it was not the winner as Lowe rescued the home side 17 minutes later.