But Cobblers were made to work hard for their victory by a well-organised Shrimps before second-half goals from Adebayo Akinfenwa and an own goal from Kevin Ellison swung the game their way.
Northampton started the brighter of the two teams with Jake Robinson having a shot blocked early on, while Chris Hackett was twice off target with fierce drives. Ellison went closest to breaking the deadlock midway through the first half when he raced away but shot against the post with Lee Nicholls well beaten.
The hosts had the better of the exchanges and Hackett saw another effort flash just past the post.
After the break, Andy Fleming had a shot blocked and Izak Reid blazed over before Akinfenwa put Cobblers in front in the 56th minute, heading home Ben Tozer's long throw-in.
They increased their lead five minutes later when another Tozer throw-in was headed past Barry Roche by Ellison.
Morecambe never recovered from the setback and Ishmel Demontagnac rounded it off with a third goal in stoppage-time, curling in a great free-kick.