Gylfi Sigurdsson kept his cool from the spot as Crewe grabbed a draw after trailing 2-0 in the first 20 minutes.
Keeper John Ruddy, left stranded by a deflected Aaron Wilbraham shot for the first, then allowed a weak Jason Puncheon effort to sneak in.
Mark Carrington's 77th-minute header brought Crewe back into contention.
Three minutes later they were level when on-loan midfielder Sigurdsson converted a spot kick after keeper Willy Gueret had felled Alan Sheehan.
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Milton Keynes Dons: Gueret, Regan, O'Hanlon, Llera, Lewington, Chadwick (Johnson 46), Howell, Leven, Puncheon, Baldock, Wilbraham.
Subs Not Used: Abbey, Stirling, Gerba, Navarro.
Booked: Gueret, O'Hanlon, Howell, Leven.
Goals: Wilbraham 15, Puncheon 19.
Crewe: Ruddy, Brayford, Baudet, Woodards, Broomes, Sheehan, Carrington, Sigurdsson, Donaldson, Pope (Miller 71), Grant (Moore 57).
Subs Not Used: Collis, O'Donnell, McManus.
Booked: Grant, Brayford, Pope.
Goals: Carrington 78, Sigurdsson 82 pen.
Att: 8,454
Ref: James Linnington (Isle of Wight).
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