It was all about penalties at Prenton Park as Oldham extended their unbeaten away record to 13 games.
Oldham scored one from the spot and Tranmere missed one at a time when they would have gone ahead.
It was a ding-dong affair. The Latics broke the deadlock in the 37th minute after Gareth Roberts floored Wayne Andrews in the box.
Skipper David Eyres netted from the spot with an excellent left-foot shot into the keeperÂ’s left-hand corner.
Tranmere levelled in the 59th minute with a 12th goal of the season by Simon Haworth, who found the net with an angled header from a cross by Alex Hay.
In the 67th minute OldhamÂ’s Will Haining was adjudged to have handled in the box following a Roberts free-kick.
Roberts, who had been booked when he conceded a penalty, stepped up for Rovers, but his shot towards his top left-hand corner was brilliantly turned aside by keeper Les Pogliacomi.
Oldham regained the lead in the 76th minute with an exquisite header by Julian Baudet from a Paul Murray Cross.
The visitors almost had a third on 84 minutes, but an angled shot by Andrews rebounded off the foot of a post.
"The holiday period has gone well for us," said Oldham boss Iain Dowie. "We were much the dominant side and it is a fantastic result.
"The penalty against us was an absolute joke and it was justice that it was saved." Tranmere manager Ray Mathias felt his side had been dominant: "I feel as though we have been mugged. It is very frustrating.
"The lads played exceptionally well, but it is all about goals and you have got to give credit to Oldham."