Lawson D’Ath, Sam Hoskins and Joel Byrom put The Cobblers well in command at the Globe Arena before Tom Barkhuizen pulled a goal back.
Any hopes of a comeback were shortlived however as Dominic Calvert-Lewin added a fourth with Shaun Brisley’s late own goal not enough to stop The Shrimps’ run of victories ending at four.
The convincing triumph for the visitors also means Morecambe have just one win in 13 games against The Cobblers in League 2.
Both sides looked bright in an even opening.
The best fans photos from Preston North End's 4-1 win over Huddersfield Town in the Carabao Cup.
Player Ratings: Huddersfield Town 1-4 Preston North End - Carabao Cup win on the road
Tottenham Hotspur loanee impresses Preston North End boss as plan comes together in Carabao Cup demolition of Huddersfield Town
Match Report: Huddersfield Town 1-4 Preston North End - PNE turn on the style in the Carabao Cup
A performance that Preston North End should back up -Tom Sandells' verdict after Carabao Cup win at Huddersfield Town
Aaron Wildig tested Adam Smith with a shot from 20 yards on the half-volley after a fine team move before some more flowing football saw the Northampton stopper called into action by a Kevin Ellison volley.
The Cobblers were always in the game though, Barry Roche saving well after Calvert-Lewin flicked Hoskins’ cross goalwards from close range midway through the half.
Adam Dugdale then had to be on hand to clear from inside his own six-yard area after Roche had flapped at a corner and D’Ath fired in a shot.
The set pieces kept coming with Calvert-Lewin failing to capitalise on a free header and Nicky Adams curling in an effort from 20 yards as the ball broke that was well saved by Roche.
Morecambe continually couldn’t clear their lines however and the opening goal came on the half hour.
Adams got the better of Wildig down the left and fired in a cross that D’Ath volleyed home from close range.
The hosts were rocking and they went further behind three minutes later.
Captain David Buchanan broke at pace but his cross should have been cleared by Laurence Wilson, The Shrimps defender slipping allowing Hoskins the time and space to take a touch and finish well beyond Roche from 12 yards.
The hosts weren’t lying down though, Ellison seeing a header from a Shaun Beeley cross hacked off the line by Ryan Cresswell.
Devitt then whipped a shot onto the roof of the net as The Shrimps counter attacked at pace.
Any hopes Morecambe had of a comeback were dealt a major blow two minutes into the second half however.
Byrom whipped in a free-kick from the right with the left-footed centre evading everyone and sneaking into the far corner.
It should have been four shortly after but Roche produced a fine double save to deny Adams and Calvert-Lewin before The Shrimps hacked clear.
Northampton kept coming as they threatened to run riot, Roche saving point-blank to deny Hoskins a second.
Morecambe crucially got the game’s next goal on 66 minutes to give themselves a glimmer of hope.
Devitt sent across the corner with Barkhuizen rising unmarked to head home from 10 yards.
The joy was shortlived however with Northampton restoring their three-goal advantage two minutes later.
The Cobblers countered at pace with substitute Alfie Potter squaring for Calvert-Lewin to flick home at the near post.
Morecambe kept coming but were wide open at the back, Potter bringing a save from Roche with his legs.
Brisley then saw an effort from close range deflected over as the hosts failed to deal with a corner.
And It wasn’t to be the big central defender’s final involvement in the game as he inadvertently deflected Ellison’s cross beyond Smith five minutes from time to reduce the arrears to two.
But it mattered not as The Cobblers joined The Shrimps on 13 League 2 points.
Morecambe: Roche, Beeley (capt), Dugdale, Edwards, Wilson (McGowan 82), Goodall (Mullin 57), Fleming, Devitt (Molyneux 73), Wildig, Barkhuizen, Ellison. Subs not used: O’Hara, Miller, Ryan, Parrish.
Northampton: Smith, Furlong, Cresswell, Brisley, Buchanan (capt), Byrom, Watson, D’Ath (O’Toole 90), Hoskins (Potter 63), Adams, Calvert-Lewin. Subs not used: Clarke, Richards, Lelan, Corry, Hackett.
Referee: Eddie Ilderton
Attendance: 1,778 (327 away)
Look back at the game with our Shrimps Live blog
Shrimps Live is the home of our Morecambe FC coverage this season with live match updates and breaking news throughout the week.
Join the debate on Twitter using #shrimpslive