They faced a resurgent Boro side under new head coach Aitor Karanka and were soon behind as Knight lost the ball when trying to play out from the back and the impressive Carayol fired past Andy Lonergan from 20 yards.
After Chris Eagles went close to equalising, Knight's pass back to goalkeeper Lonergan was badly over hit and gave Main a tap-in on the line.
Bolton gave themselves hope as Baptiste curled a shot from just inside the penalty area past a helpless Shay Given.
The goal inspired Dougie Freedman's side in the second half and after Cardiff loanee Mason had fired into the side netting, Ngog sealed a dramatic finale with a late leveller.
Bolton manager Dougie Freedman:
"Once again we shot ourselves in the foot and gave them a 2-0 lead. We then showed great character and spirit and I believe that we did enough to eventually win the game in the end.
"Zat Knight will take it on the chin and after the mistakes there wasn't much else he did wrong in the game. He stood up and did well.
"Nobody's put a bid on the table for any of my players and David [Ngog] is a good young lad who's done well in training and took his chance today when he came on.
"I have to make sure we're strong on the football field, but we've got financial fair play in place so we have to cut our cloth accordingly."
Middlesbrough head coach Aitor Karanka:
"Today is the worse we have played since I came to the club. I was disappointed that we could not hold on for the win, but I think that we didn't deserve to go 2-0 up and I'm sure that we can play much better than we did do today.
"We had no possession of the ball and we weren't comfortable on the pitch. We need to have the possession of the ball to keep them away from the counter-attacks.
"We played thinking that we were better than we are and we needed to play like we did in the previous three games."
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