The midfielder slipped unmarked into the box to clip a shot past goalkeeper Sam Slocombe after the home side had looked set sneak all three points themselves.
After a poor first half, the gameonly came to life after the interval and three times in a minute it was the visitors who could have snatched the lead.
First a close-range effort from Brian Woodall was turned away at full stretch by keeper Slocombe.
From the corner that followed Josh Scott headed against the foot of a post and before Scunthorpe could clear their lines a goal-bound effort by Howell was blocked away by a desperate home defence.
Scunthorpe perked up after the introduction on the hour of veteran striker Chris Iwelumo, but nine minutes later he missed a golden chance to open the scoring when he saw his poor 69th penalty easily saved by goalkeeper Chris Lewington after a handling offence by full-back Femi Ilesanmi.
Iwelumo then missed another good chance with a close-range header before centre back David Mirfin seemed to have plundered victory for Scunthorpe in the 88th minute when he headed home a corner from Andy Dawson.
But in the second minute of stoppage time Dagenham equalised with the first goal Scunthorpe have conceded this season.