Jake Reed shot over early on for the Daggers while Ben Tozer was off target with a long-range effort for Northampton, for whom Lewis Hornby also had a goalbound shot blocked.
The Cobblers found it difficult to break down the Daggers defence and it took an own goal from Abu Ogogo to gift the hosts a 36th-minute lead, the visiting skipper turning Clive Platt's flick-on past 'keeper Chris Lewington.
Either side of the opener, Dagenham's top scorer Sam Williams squandered a couple of good chances, missing the target following hesitancy from Kelvin Langmead and then heading over from Medy Elito's excellent cross.
And the second miss proved crucial as Cobblers quickly doubled their advantage in the 39th minute, Chris Hackett racing into the box to beat Lewington with a neat finish.
Dagenham responded well after the restart and had a couple of chances to reduce the arrears, Matt Saunders going close and substitute Brian Woodall's header hitting a post.
But Langmead put the result beyond doubt seven minutes into the second half, getting on the end of another Tozer delivery to head past Lewington.
Scott Doe should have done better with a header for Dagenham, who continued to create chances to get back into the contest. And it was the Daggers defender who finally reduced the arrears in the 71st minute with a low drive following some poor defending from the hosts.