David Ball was the most high profile casualty of the battle at Sixfields - won by a late Luke Norris free kick.
The striker suffered a suspected dislocated shoulder as Fleetwood faltered against a rugged and determined Cobblers side.
Ball nearly put Fleetwood into an early lead, rattling the woodwork after a lovely turn from a Gareth Evans cross.
It was tough going against a Cobblers side who didn’t give an inch and played with little finesse but plenty of passion.
Not that they created many chances, the best of the first half for the home side coming from Chris Hackett’s cross, nearly turned past his own keeper by Jef Hughes.
After the break Fleetwood upped the tempo but couldn’t convert despite making numerous half chances.
And they were punished at the death.
A free kick, inside the D, Norris lifting it over the wall and into the top corner.