Freddie Ladapo put the hosts in front with his 17th goal of the season after 10 minutes as the Millers looked to move three points clear of Coventry City, who host Sunderland tomorrow afternoon.
But MK Dons hit back 12 minutes later when Rhys Healey fired in the equaliser after getting in behind the United defence.
Paul Warne made one change from the side that drew with Coventry in midweek, with Dan Barlaser forced to the sidelines by an ankle injury as Jamie Lindsay started for the first time since December.
Michael Smith almost restored the Millers' advantage but his header from Ben Wiles's corner dribbled wide of the post.
The Rotherham forward was then denied superbly by Lee Nicholls who pulled off a point-blank save to keep the scores level.
Ladapo missed a fantastic opportunity to regain the lead in the second period but his shot clipped the outside of the post from close range.
Wiles almost got the hosts ahead but his curling effort shaved the outside of the post as MK Dons held on for the point.
Rotherham remain top of League One but are just one point ahead of second-placed Conventry who have two games in hand.