Stoke scored twice in the closing minutes to snatch a dramatic late victory.
But it was a real heart-breaker for Scunthorope, who looked set for all three points themselves after dominating much of the game.
It was the visitors who went in front after 26 minutes with a disputed goal when Richard Cresswell applied the finishing touch from close range to a cross from Danny Pugh, with the home defence appealing in vain for offside.
But Scunthorpe were back on level terms just five minutes later when striker Paul Hayes rifled in a right-foot shot after an earlier effort from Cleveland Taylor had been half-blocked by centre-back Ryan Shawcross.
The home side were desperately unlucky not to go in front in the 38th minute when they were twice denied by the woodwork.
First, a dipping shot from the edge of the box by Hayes crashed back off the bar and, in the scramble to get it clear, Shawcross too turned the ball against his own bar.
Stoke's main threat upfront came from the pace of Ricardo Fuller and he wasted a glorious chance to put his side back in front early in the second half.
Midfielder Liam Lawrence should also have done better with a clear-cut chance.
But Scunthorpe were forcing most of the pace and creating plenty of chances themselves with Hayes and Kevan Hurst both going close.
Scunthorpe thought they were on their way to victory when midfielder Jim Goodwin fired home a glorious right-foot shot to put them 2-1 in front in the 85th minute.
But three minutes later, Stoke were handed a lifeline when Scunthorpe striker Hayes turned a low right-wing cross from Lawrence into his own net.
In stoppage time, the visitors then went on to snatch victory for themselves when Lawrence headed home a terrific left-wing cross from Pugh after Scunthorpe had been caught out on the break.