City, who moved above the Cobblers off the back of the win, shaded the first half and went in front after 22 minutes.
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.
- Sports & Recreation
- Jamie Cureton