A Marvin Sordell penalty secured the points while Jonathan Woodgate was dismissed for the visitors.
The Trotters were made to chase victory without Jay Spearing (broken toe) and striker David Ngog (dislocated shoulder), while Boro were lacking the services of Merouane Zemmama and striker Lukas Jutkiewicz but centre-back Woodgate passed a late fitness test on a tight muscle.
The Boro defence were nearly breached within the first two minutes when Bolton's Craig Davies tried a speculative 18-yard shot that Jason Steele did well to tip around the post.
Barely 60 seconds later Steele was in the action again, tipping over from Medo following Chris Eagles' corner.
Boro looked against the ropes but ventured outside their own penalty area to fashion an opportunity after nine minutes, Scott McDonald's 25-yarder causing Bolton goalkeeper Adam Bogdan some moments of concern as the hosts eventually cleared their lines.
McDonald tried his luck again from distance six minutes later but this time was well wide from a similar distance.
Boro were having their fair share of possession, though, and McDonald should have done better when presented with a headed chance just six yards from goal after 23 minutes.
At the other end, Woodgate's foul on Chung-Yong Lee saw the hosts given a shooting chance 35 yards from goal but Marcos Alonso's well-struck effort was held comfortably by Steele.
Bolton still looked the more likely to break through and after 27 minutes Darren Pratley went close again from distance before Davies tried his luck again.
The visitors were the first to show after the interval when a shot from Mustapha Carayol from 20 yards brought a desperate stop from Bogdan, but the Trotters broke the deadlock on their next foray upfield.
Lee's pass provided the opportunity and from 12 yards out, Eagles made no mistake for his 10th goal of the season to make it 1-0 after 50 minutes.
But if the hosts expected Tony Mowbray's men to roll over they were proved way off the mark six minutes later when McDonald crossed from the left and Kieron Dyer headed home from six yards out for the equaliser.
Parity lasted a mere three minutes, though. Woodgate's foul on Lee resulted in a booking for the former Leeds man and a penalty, from which Marvin Sordell restored the hosts' lead.
Five minutes later another Woodgate foul - this time on Sordell - saw the Boro man dismissed and the visitors' hopes effectively disappear.
Bolton almost added to their tally with 10 minutes left but Steele did well to keep out another effort from distance by Sordell.
- Sports & Recreation
- Jonathan Woodgate
- Marvin Sordell