Brian Stock pounced in the fourth minute of added time to condemn Boro to a ninth away loss this term.
Middlesbrough, who have now taken just four points out of a possible 33 on their travels, made a flying start when Scott McDonald put them ahead inside four minutes, but James Hayter levelled in the 22nd minute.
Mowbray said: "I thought in the last 20 minutes of the second half we were the only side that were going to win the game, so we were absolutely gutted to lose like that.
"We missed a few chances, but I suppose at one point because of the way we played we wouldn't really have been content with the draw, but then we end up losing."
Source: PA
Source: PA