Tuesday night's two-goal hero Emile Sinclair started on the bench as another recent signing, John Marquis, started the game in attack.
Northampton enjoyed their fair share of the ball in the opening 45 minutes but found chances hard to come by as Fleetwood threatened on a number of occasions, Gareth Evans netting the opening goal midway through the first half.
Sinclair entered the fray just after the break, replacing Antonio German up front for the Cobblers who enjoyed their most threatening spell of the game around the hour mark, Matthias Kouo-Doumbe coming close with a header.
Chris Wilder then went for broke by bringing Alan Connell on for midfielder Ricky Ravenhill but the home side regained their control of the game and made it safe when Evans score his second with ten minutes to go.
Defeat for Torquay and the postponement of games involving Bury and Wycombe mean Northampton don't lose any ground at the bottom but another game has gone in their bid to remain in the Football League.