Andy Mangan's injury-time header gave Fleetwood a fourth win in a row against 10-man Northampton.
Daniel East received his second yellow card for the Cobblers after 29 minutes when he fouled Jamie McGuire.
McGuire had two headers disallowed for offside and Fleetwood could have felt it was not their day when Junior Brown's goal was also ruled out.
However, Mangan nodded in at the back post in the second minute of stoppage time to give the Cod Army the points.
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Northampton Town manager Aidy Boothroyd told BBC Radio Northampton:
"I thought we should never have had a man sent off in the first place.
"It wasn't a foul (the first booking). He wasn't going off until the Fleetwood players got around.
"That's not me having a go at the Fleetwood players, that's just gamesmanship and that's where the referee has to be strong and deal with it.
"But there you are. He wasn't, he didn't and the boy went off. But after that they worked their socks off and so we're disappointed not to come away with something."