With the clock ticking away it seemed that Tranmere would deny Scunthorpe that play-off place as they led by a 39th-minute goal from Craig Curran.
He was on hand at the far post to head home a perfect cross from Ian Moore.
Five minutes later Tranmere almost struck again with Moore again providing a cross from the right which saw Steve Jennings get in an acrobatic shot that was brilliantly turned away by keeper Josh Lillis.
The visitors had bossed the opening half in this 'winner take all' clash between the two teams battling for the one remaining play-off spot.
But Scunthorpe came storming back in the second half to put Tranmere under pressure.
But they couldn't find their finishing touch in front of goal with 30-goal leading marksman Gary Hooper missing a hat-trick of openings. Fellow striker Paul Hayes also went desperately close.
It was skipper Byrne who rescued his side a priceless point when he headed home a free-kick that was knocked high into the box by Grant McCann for his second goal in successive games.
It came just after the visitors had been reduced to ten men when defender Gareth Edds was sent off by referee Steve Tanner for a second bookable offence.
It was desperately hard luck on Rovers who looked comfortably in control for long spells but they were unable to snatch the winner they needed as the game drifted into four minutes of stoppage time.
Scunthorpe now go forward to face MK Dons in the two-legged play-offs.
But they have injury problems piling up with full-backs Andrew Wright and Joe Mills both doubtful starters after picking up knocks which forced them to be substituted.
Wright was described as having an "horrific facial injury" by the Iron manager Nigel Adkins, and is highly unlikely to feature in Friday's first leg.