The Cobblers looked set for a vital three points after being handed the lead in the first half but a late Morecambe rally denied them victory.
Northampton were gifted the lead in the 44th minute through a nightmare own goal from Andy Wright.
Emile Sinclair crossed from the right and Wright's attempt to clear ended with him slashing the ball past his own goalkeeper Barry Roche.
The home side hit back in the second half with Matt Duke making a world class save to tip away a Kevin Ellison free-kick.
But Morecambe's pressure paid off in the 76th minute when Padraig Amond, who had hit the post in the first half, finished a fine move with a right foot-shot from 12 yards out.
Both sides went close to winning the game in the final minute.
Ian Morris had a shot scrambled off the line by the Morecambe defence before Jamie Devitt beat Duke to a loose ball but saw his shot creep inches wide of the right-hand post.