Freddie Ladapo netted his fourth goal in as many matches and 17th of the season to put the Millers ahead early on when he ran in on goal from Jamie Lindsay’s pass and powered an effort past Lee Nicholls.
However, after Rhys Healey had drawn MK Dons level in the 22nd minute, Ladapo spurned an easy chance to win the game in the second half.
Michael Smith had two great opportunities to restore Rotherham’s lead but he headed wide from a corner before being denied by Nicholls.
Ladapo missed an even easier chance as he inexplicably dragged wide from close-range.
Ben Wiles also went close with a long-range curler but Rotherham also needed goalkeeper Daniel Iversen to deny Alex Gilbey in stoppage-time.
Millers chief Paul Warne said: “It’s disappointing we haven’t won it. This season, whenever we’ve got a second goal we’ve usually gone on to win handsomely.
“This point doesn’t feel a good point but it might be at the end of the season. The lads gave everything. With a bit of luck, we could have won the game.
“Freddie will be disappointed. He is allowed to miss one now and again. Had it been 3- or 4-1 we wouldn’t be talking about it. There is not much I can complain about apart from we didn’t get the second goal.”
Rotherham United: Iversen, Olosunde (MacDonald 90), Ihiekwe, Wood, Mattock, Ogbene, Crooks, Lindsay (Koroma 73), Wiles, Smith (Vassell 73), Ladapo. Unused substitutes: Thompson, Price, Adelakun, Tilt.
Milton Keynes Dons: Nicholls, Poole, Walsh, Moore-Taylor, Williams, Houghton, Thompson (Kasumu 67), Gilbey, Brittain (Gladwin 67), Nombe (Mason 81), Healey. Unused substitutes: Cargill, Reeves, Fisher, McGrandles.
Referee: L Doughty (England).