They might have gone ahead early on but Jonathan Forte was ruled a foot offside and then David Mirfin rose perfectly to meet a free-kick from Josh Wright, only to be denied by Adriano Basso's superb dive.
City's loan signings Evander Sno from Ajax and Costa Rican striker Alvaro Saborio had worked a free-kick which saw the ball in the net, but Saborio had been flagged offside in a very tight decision.
With Nicky Maynard testing United's keeper Joe Murphy with a shot drilled from 25 yards, the first 20 minutes or so saw the game buzzing.
As the sparkle faded Scunthorpe's manager Nigel Adkins divided his time between the touchline and a seat in the stand.
Both sides developed their game from pacy thrusts from midfield, with Sno giving City a slight edge, although without a winger they lacked width.
When the deadlock was broken early in the second half it was a devastating moment of bad luck and muddle for the visitors.
A clearance by left-back Marcus Williams struck team-mate Sam Togwell and bounced to Saborio, who scrambled in his first goal for City at the second attempt.
It spurred Scunthorpe's manager into sending on his three subs, a move which misfired when the first of them, Gary Hooper, limped off with a muscle injury leaving Scunthorpe with ten men for the final ten minutes.
City decided to tighten up but Scunthorpe had not given up.
Basso made a flying save to prevent Paul Hayes from scoring, but in injury time the visitors got the draw they deserved.
A weak defensive header from Jamie McCombe was seized on by sub McCann, who stunned City with the aid of a deflection.