Substitute Enoch Showunmi's 69th-minute goal won it for Bristol City with a delicate touch which seemed so much out of keeping with his size.
His height of 6ft 6" makes the recent signing from Luton an obvious target man but his goal 20 minutes from the end was entirely fashioned on the ground.
Moving on to a flick by another new City player, ex-Yeovil striker Phil Jevons, he rounded one defender and then the goalkeeper before steering the ball gently home.
Gary Johnson's side are facing another season in League One and their frustrated mood was not eased when two early shots bounced away off the bar.
The first was set up by Craig Woodman's speedy break down the left and a deep cross which Stephen Brooker steered away from Scunthorpe's new keeper, Joe Murphy but not away from the woodwork.
The second came from distance as the impressive Cole Skuse's shot rose a fraction too high, grazing the upper side of the bar as it flew into the stand.
City laid out their stall early, attacking down the flanks but not finding the accuracy of shot to finish. Jevons, signed in the summer by his former manager, needed all the reassurances Johnson could offer after he struggled in the first half.
His only shot of note was always flying off target but after making the opening for Showunmi his game ended when he was pulled off in a tactical switch.
Scunthorpe were content to soak up the pressure as they tried to work out how to bring their high-octane strikers Billy Sharp and Andy Keogh fully into action but Louis Carey superbly marshalled his back four.
Late on Scunthorpe threw on former City striker Steve Torpey in an attempt to pull-back the goal but he was in action for only eight minutes before being red-carded for a challenge on Carey. A card was inevitable, red looked harsh.
Even so Scunthorpe still came close to saving the game when Ian Baraclough's shot was turned around the post by Brazilian keeper Adriano Basso and with it their chance of a share of the spoils.