The Dons suffered a fourth straight loss for the first time since December 2009, as they went down 2-1 to Leeds at Stadium:mk.
The West Yorkshire outfit took the lead just past the half-hour mark when Chris Wood found the target from close range.
Baker pulled down Charlie Taylor inside The Dons’ penalty box, and striker Wood made no mistake from 12 yards.
Taylor made it 2-0 to Leeds just before the half-time interval when he found the target with his left foot.
Simon Church halved the deficit for the hosts in the 74th minute, but Karl Robinson’s side ended the game with 10 men following the sending-off of Samir Carruthers.
Attacker Baker has taken to Twitter to express his disappointment and has accepted responsibility for his role in The Dons’ defeat.
Gutted. Gave away a pen! Hurt my ankle and lost! Not a great day! Thought we deserved more than we got again tho. Fans were great, sorry!— Carl Baker (@Carlbaker_mkd7) September 19, 2015