Patrick Bamford scored a stunning late winner to spare the Dons' blushes after the 10-man Millers had battled back from two goals down to equalise.
Evans was sent to the stands at half-time for an incident in the tunnel and he felt Barclays Premier League referee Madley got a number of decisions wrong on the day.
He said: "I'm very proud of the players. We were the better team, there were some super performances, but we've lost the game.
"We didn't think it was a penalty, we've seen it again and there was no contact.
"Then he sent me off for shouting - there was no abusive language.
"He's come and knocked on my door just when we were about to go back out and told me to go upstairs.
"I'm really disappointed with some of the things that went against us - the players are devastated.
"I don't question the integrity of Robert Madley, he's an honest man, but we've had many decisions go against us now this season.
"But it's soul-destroying to miss the chances we missed.
"The luckiest team on the planet just now are MK Dons - everything that could have gone their way has gone their way.
"But we'll take it on the chin and bounce back, we have no alternative."
Shaun Williams put the Dons ahead on the stroke of half-time when his low spot-kick squirmed underneath Scott Shearer after O'Connor had been sent off for tripping Stephen Gleeson.
Ben Reeves doubled the Dons' lead in the 65th minute, but Rotherham scored twice in as many minutes to make it 2-2, through Lee Frecklington and Tom Flanagan's own goal.
But Bamford swept the ball into the top corner from 20 yards in the closing stages to snatch the points for the Dons.
- Sports & Recreation
- Patrick Bamford
- Barclays Premier League