The home side showed promise straight from the kick-off with the wide play of Jeff Smith and Christopher Birchall causing problems.
Smith should have gifted his side a goal on 13 minutes when Simon Eldershaw crossed from the right but the winger failed to connect.
Billy Paynter went closer seconds later after he headed Ryan Brown's free-kick goalwards but David Beharall was on hand to clear the danger.
Jonathan Brain was called into action soon after with the young goalkeeper having to make a solid low save from a Kevin Betsy shot.
However, the Latics did score and after a dubious free-kick, Brain spilled the ball to present Scott Vernon with a tap in from two yards on 33 minutes.
Vale wasted no time in replying and equalised three minutes later.
Michael Cummins' 30-yard pile driver was tipped on to the cross bar but Paynter was present to knock home.
The Valiants took the lead in the 62nd minute when Eldershaw crossed from the right with Birchall this time stooping to head past a helpless Leslie Pogliacomi.
Oldham's fate was sealed on 79 minutes when Adam Griffin brought down Lee Matthews to concede a penalty.
The substitute stepped up and slotted into Pogliacomi's bottom left-hand corner to give his side the deserved victory.