The Northern Ireland international, a 67th-minute substitute, saw his 92nd-minute effort beat Adriano Basso in the City goal to extend the Iron's unbeaten run to three games after it had looked as though Alvaro Saborio's first goal in English football had given the Robins a fourth straight win on home soil.
The Costa Rica international was in the right place at the right time five minutes after the restart to help City extend their unbeaten home run to 15 games, but they were unable to take all three points thanks to McCann's late intervention.
United boss Nigel Adkins surprisingly opted to relegate Gary Hooper to the bench despite his midweek brace against Preston, but it was his replacement, Jonathan Forte, who had the first chance as he fired against Adriano Basso inside the first two minutes.
Nicky Maynard, who had scored City's previous six goals going into the game, recovered from injury in order to take his place and was soon making his presence felt too, with his low driving testing Joe Murphy in the Scunthorpe goal.
Both sides then had goals ruled out for offside, with ex-Scunthorpe man Jamie McCombe and Forte both falling foul of the linesman's flag, while Basso had to be at his best as he produced a fingertip save to claw away Martyn Woolford's header.
Paul Hayes who, unlike Hooper and Forte, has maintained his place in Adkins' starting line-up despite just one league goal this season, had the best chance of the opening half three minutes before the break, scuffing wide from two yards out after a run and cross from the lively Woolford.
Josh Wright was the next to spurn a chance for the Iron, failing to beat Basso as he broke through on goal two minutes after the break and he was made to rue his miss as City opened the scoring three minutes later.
Maynard had already had a penalty appeal turned down when the goal came after he and Murphy went for the same ball, but it was his strike partner Saborio who did the damage as he rifled home from close range after the ball fell to him following a deflection off the unsuspecting Wright.
Maynard and Saborio now had Scunthorpe's defence running scared and should have added a second just shy of the hour mark when the ball came free in the area, but the pair were unable to fashion an opening for one another.
City appealed for another penalty midway through the half, calling handball against Sam Togwell who was making his 150th career start, before Scunthorpe reminded the home side of their abilities as Hayes unleashed a close-range rocket that Basso did outstandingly well to keep out.
With Hooper off the bench but off the field injured, United ended the game with 10 men, but triumphed over adversity as McCann scuffed home a loose ball after a Wright free-kick.