John-Joe O'Toole and Ricky Holmes turned the game around after Christian Doidge had given the home side a 62nd minute lead.
Home boss John Still was pleased with his side's performance, telling BBC Radio London afterwards: "When we attacked we had more threat in our game than they did, and they're a top side, so I'm really really pleased with that."
Northampton remain second, behind Plymouth Argyle on goal difference and now seven points clear of third-placed Oxford United.