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.
VIEW FROM THE DRESSING ROOM
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."
Fleetwood Town 01 Davies 02 Beeley 03 Howell 05 McNulty 12 Brown Booked 28 Mawene 10 Fowler Booked 18 McGuire (Barkh'zen - 59' ) 20 Johnson 09 Parkin Booked (Gillespie - 30' ) 14 Mangan Substitutes 16 Maxwell 33 Eastham 08 Milligan 11 Nicholson 27 Marrow 19 Gillespie 32 Barkh'zen Northampton Town 21 Nicholls Booked 03 Widdowson 05 Langmead 12 Tozer 18 Artell Booked 23 East Dismissed after an earlier booking 08 Harding Booked 11 Hackett 09 Platt 14 Nicholls 19 Moult (Wilson - 46' ) Substitutes 13 Snedker 04 Guttridge 07 Demontagnac 24 Turnbull 15 Mukendi 16 Wilson