Rovers fought their way back into the game after falling behind to Amadou Bakayoko’s 47th minute goal on the break.
Mipo Odubeko came off the bench to score his first goal for the club but within seconds of the equaliser former Rovers winger Kieran Sadlier struck the winner for Wanderers.
Rovers had 19 shots on goal compared to Bolton’s 11.
The defeat leaves Gary McSheffrey’s side six points from safety with just three games left to play. They head to Shrewsbury Town on Monday where relegation could be confirmed.
“Their two bits of end product in the second half they score from,” said McSheffrey.
“They countered quite well and got in some good crossing positions, they fizzed a few across the six-yard box.
“But in terms of chances in the second half I think they really put their two away quite clinically.
“We’ve created some good chances today and their goalkeeper has made two or three good saves but ultimately we should be scoing at least one or two more.”
Relfecting on the game and his team’s performance, McSheffrey said: "For five or six minutes we couldn’t get near them at the start of the game and then we couldn’t retain the first ball when we won it back.
“The next time I look at the clock it’s 24 minutes and I think we got a foothold back in it, we played well, we were on the front foot, we were moving the ball well.
“Before you know it it’s half time and I thought it was a great game of football.
“Second half we started a little bit sloppy again, there was some poor decision-making.
“But we react well from the disappointment of conceding and get ourselves back in it.
“Then we need to be better. When we get back in it we need to manage it better. You can’t concede in their next attack. The lads need to learn from that.
“But in terms of the performance level I think it was a good performance. I thought the lads were brave, played on the front foot, got on the ball well and I think excited the crowd a bit and got them off their seats at times.
“We missed some big chances and their goalkeeper has made a couple of great saves.
“We’re obviously disappointed with the result but the performance level was good.”