City, who moved above the Cobblers off the back of the win, shaded the first half and went in front after 22 minutes of Saturday's League Two clash at St James Park.
Craig Woodman's in-swinging corner caused panic for Northampton goalkeeper Lee Nicholls and, with Jamie Cureton on his toes, he fumbled the ball into his own net.
Cureton should have made it 2-0 when he beat the offside trap, but he took an extra touch, which allowed Nicholls to save.
Northampton's best chance came when a cross from the right was turned towards his own goal by Scot Bennett, but Artur Krysiak pulled off a superb save to preserve Exeter's lead.
Cureton did make it 2-0 with his 20th goal of the season after 59 minutes, darting towards the near post to head in Matt Oakley's superb free-kick.
Northampton's Adebayo Akinfenwa saw a header cleared off the line by Arron Davies, but Jake Gosling wrapped up the points for Exeter eight minutes from time with a brilliant individual goal, his first for the Grecians.