Conceding goals has been a problem all season for the Essex side and it was more kamikaze defending which let them down again.
With veteran striker Teddy Sheringham ruled out with a toe injury from what would have been the final game of his career, Colchester struck first in the 11th minute when Kevin McLeod met a left-wing cross from Kevin Lisbie with a glancing header past goalkeeper Joe Murphy.
But Scunthorpe were back on level terms four minutes later when winger Jonathan Forte scored from close range - his first goal since last December.
It was Colchester that came storming out in the second half to seemingly take command of the encounter.
Striker Scott Vernon fired them 2-1 in front in the 47th minute with a brilliant overhead kick and, 60 seconds later, McLeod plundered his second goal of the game after some poor defending by the home side.
Paul Hayes earned Scunthorpe a lifeline when he reduced the arrears in the 67th minute with a shot on the turn in a crowded box.
And it was Hayes who then snatched an 82nd-minute equaliser for Scunthorpe when he intercepted a headed back pass from Matt Heath and took the ball around keeper Dean Gerken to finish his own season on a high with his fifth goal in the last three games.
Both these teams will now need to re-group during the summer as they prepare for life back in League One.