Recent signing Ricky Holmes broke the deadlock on the hour mark, fair reward for Chris Wilder's side who had created the best of the chances prior to that.
Town pushed on after the goal in their bid to make the game safe, Lawson D'Ath coming closest to a second goal when he hit the bar on 83 minutes.
Dagenham threw caution to the wind in the final minutes and Joss Labadie came close, denied by Matt Duke in the Northampton goal.
4,122 watched a crucial win for the hosts, continuing the upward momentum of recent weeks and again proving Wilder correct in his revamp of the squad at the beginning of January.