Leading marksman Gary Hooper also missed a great opening for the home side as MK Dons looked to be wobbling under early pressure.
But they forced their way back on to level terms with their first real effort of the game when striker Aaron Wilbraham squeezed a close range header into the roof of the net after Scunthorpe had failed to clear a corner.
The visitors started the second half strongly with Wilbraham denied a second goal by a good block from makeshift full back Ian Morris.
Scunthorpe thought they had gone back in front on the hour when Hooper netted from close range, only to be denied by a linesman's flag for offside.
In a pulsating finish both teams had a chance to nick a lead for next week's second leg.
Scunthorpe striker Hayes had a shot well turned away by Gueret and from the corner that followed the French keeper excelled again, somehow keeping out a shot from substitute Krystian Pearce from point blank range.
But in the final minutes it was MK Dons who nearly snatched a winner when first Wilbraham saw his goalbound shot blocked away by defender David Mirfin and then substitute Sam Baldock was denied by a last gasp save from keeper Joe Murphy who minutes later, had to hobble off with a recurrence of groin trouble.