Kevin Thornton’s first-half strike separated the sides at the break, with the midfielder scoring from close range after the Shrimps had failed to clear Michael Jacobs’ cross.
The Cobblers could have won the game by a greater margin if they had taken their chances. Guillem Bauza
missed two open goals and Shaun Harrad wasted two excellent openings in the second half.
Morecambe rarely tested Chris Dunn but Scott Brown spurned a golden chance on 64 minutes when he missed the target from six yards after Phil Jevons teed him up perfectly.
Northampton made it 2-0 six minutes from time when Ben Tozer beat Barry Roche with a superb right-foot drive from 20 yards that flew into the top-right corner.
Morecambe set up a grandstand finish, though, with Nile Cowperthwaite heading home after 90 minutes.