Gillingham hopes of securing a League Two play-off place were extinguished after drawing at Northampton.
Lewis Wilson opened the scoring for the Cobblers when he smashed in a rebound after Paulo Gazzaniga parried Toni Silva's shot.
Jo Kuffour pounced on Danny Kedwell's cross to make it 1-1 after Neal Kitson failed to clear.
Lewis Montrose dallied on a good effort to put the visitors ahead, while Brett Williams headed over for the Cobblers.
Northampton Town manager Aidy Boothroyd told BBC Radio Northampton:
"I thought it was a bit of a burst balloon today. I expected us to do better.
"When we have games like this it highlights that we are not far away but it also highlights what we need to do.
"I want a full pre-season and I want them much, much fitter.
"I want to get a more athletic vibe around the place I want us to be fit and out-run teams and score goals late."
Gillingham manager Andy Hessenthaler told BBC Radio Kent:
"It wasn't about today, it was about the season. Even at the death a point would have taken it into the last game but Crewe scored late on and that put it to bed.
"We got a goal and I thought we could go on and get the winner but in the end we just missed out.
"We have conceded some sloppy goals, decisions haven't gone for us but as a group we've given silly goals away.
"That's what's cost us, inconsistency."