Cliff Byrne played a captain's role for Scunthorpe as they dramatically clinched a Coca-Cola League One play-off place, while Crewe and Northampton were relegated after defeats.
Tranmere knew only a win against Scunthorpe at Glanford Park would see them leapfrog their rivals into sixth and they looked set to achieve the desired result thanks to Craig Curran's 39th-minute goal.
But Byrne popped up to head in the equaliser two minutes from time after Gareth Edds had been sent off.
Scunthorpe will face Milton Keynes Dons in the play-off semi-finals, the Dons beating already-relegated Hereford 1-0 thanks to Luke Howell (85), while Leeds meet Millwall in the other two-legged clash.
United condemned Northampton to relegation by beating the Cobblers 3-0 at Elland Road, Luciano Becchio (44), the prolific Jermaine Beckford (59) and Robert Snodgrass (90) netting.
Crewe always looked unlikely to escape the drop with champions Leicester their final-day opponents, and the Foxes ended the season in style with a 3-0 win.
Bruno Berner (56), Lloyd Dyer (66) and Matty Fryatt (68) hammered the nails into Crewe's coffin, although as it turned out even a win would not have been enough to keep them up.
Carlisle were the big winners on the day as brilliant goals from Graham Kavanagh (7) and Paul Thirlwell (50) ensured United, who started the match in the bottom three, beat Millwall 2-0.
Brighton guaranteed their safety with a 1-0 win over Stockport, veteran Nicky Forster netting the only goal 17 minutes from time, while Hartlepool also escaped despite a 4-1 defeat by Bristol Rovers.
Jo Kuffour (3) and Darryl Duffy (5) set Pools' nerves jangling, and Rickie Lambert (46) and Aaron Lescott (48) repeated the trick at the start of the second half after Daniel Nardiello had pulled one back (28).
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