It was tough on the Victoria Road hosts, who battled until the end, but John Still's struggling side remain without a win so far this season.
Dagenham had the better of an entertaining but goalless first half. Brian Woodall fizzed an early shot narrowly wide, before the Cobblers replied with veteran Akinfenwa seeing a close-range header just miss the target.
Northampton's on-loan Wigan goalkeeper Lee Nicholls then produced a couple of great saves. He dived to beat away Medy Elito's well-struck shot, then similarly got down well to keep out Mike Spillane's drive from the edge of the box.
Akinfenwa broke the deadlock for the visitors five minutes after the restart. The big striker slid in to guide Chris Hackett's cross past Chris Lewington from close range.
Akinfenwa then came close to making it 2-0 in the 67th minute when he guided a header onto the post.