Carlisle missed out on the play-offs to Stevenage after goals from James Tarkowski and Oumare Tounkara sealed Oldham's first victory in nine games.
After a goalless first half in which Tarkowski headed against the crossbar, Oldham took the lead through the same player with the defender heading in.
Carlisle levelled after Tom Taiwo planted home an eight-yard header.
But Oldham snatched the winning goal when substitute Tounkara headed in Filipe Morai's corner from six yards.
The Cumbrians kicked off with hope of grabbing sixth spot, but even a Boundary Park victory would not have been enough due to the results at Notts County and Stevenage.
VIEWS FROM THE DRESSING ROOM
Carlisle United manager Greg Abbott told BBC Radio Cumbria:
"Whilst we're a bit disappointed today, we look at the big picture and we have to take a lot going forward.
"I think with Lee's injury, we miss his presence, we miss his height, we miss his ability to get us high up the pitch. We've tried all sorts of things to try and get over that and maybe it's something we're going to have to look at.
"With the resources, you go to other clubs and see Chris O'Grady, Ryan Lowe and Clinton Morrison all sat in the stand, not even on the bench and you're slightly envious as a manager."