Howell 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 game only 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 fullstretch 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.
A cross into the box was handled by Femi Ilesanmi but Iwelumo's poor penalty was saved by Lewington.
Iwelumo then missed another glorious chance with a close-range free header but the Iron thought they'd snatched it with two minutes to play.
Centre back David Mirfin powered home a corner from Andy Dawson, but the Iron switched off and Dagenham snatched a fully deserved point with a last gasp goal.