Stephane Sessegnon broke the deadlock when he swivelled and shot first time past Jussi Jaaskelainen.
Darren Pratley had a chance to equalise but goalkeeper Simon Mignolet stood tall and made the block.
Nicklas Bendtner made sure of the points in injury time, scoring from 10 yards after good work from Sessegnon.
Despite losing their first four home Premier League matches so far this term, it was Bolton who started the brighter with Pratley going close to finding the net on 13 minutes.
David Ngog was released down the right and, after a good run, he squared to Pratley, but his first-time effort went just wide.
The duo combined again on 33 minutes, again to no avail. Ngog did well to win the ball and pick out Kevin Davies who played a neat ball through for Pratley, but he slipped just as he went to collect and the danger was cleared.
The visitors got more into the game the longer the half wore on and had their best chance to open the scoring on the stroke of half-time.
John O’Shea met a free-kick from Sebastian Larsson on the left but his powerful header went wide of Jaaskelainen’s right-hand post.
Sunderland came out the stronger in the second half, nine corners backing up their dominance, but at times it seemed like neither side would break the deadlock.
Kieran Richardson bought a double block out of the Bolton defence on 52 minutes, when he was played in by Sessegnon.
His first effort was blocked by Dedryck Boyata, who threw himself into the path of the shot, before David Wheater deflected his second effort over the bar.
David Vaughan and Sessegnon then both went close before Connor Wickham hit the post – his cross-shot having beaten Jaaskelainen.
The breakthrough finally came with eight minutes to go when Sunderland deservedly took the lead.
Paul Robinson failed to clear a corner from Larsson on the left, O’Shea headed the ball back across the box and a touch from Wes Brown played it into the path of Sessegnon, who turned and shot past Jaaskelainen.
Bendtner then made sure of the points in injury time after more good work from Sessegnon. A bursting run opened up the defence before he played in the Danish striker, who coolly slotted home for his second goal for the club.
Bolton manager Owen Coyle: “The bottom line is wherever we sit just now is certainly not where I want to be as Bolton Wanderers manager.
“Because of that start these games take on extra significance because of the stigma involved in being in the bottom three, you want to be out of there and moving up, and that’s why today was a great opportunity to do it.
“What we must do is not feel sorry for ourselves. We’ll look to address what the problem was and get up and running again as quickly as we can.”
Sunderland manager Steve Bruce: “We wanted them to try to enjoy it and let me do the worrying and thankfully they’ve responded in the right way. We played very well in the second half, which was pleasing.
“There were times where I thought it was going to be one of those afternoons but, in the second half in particular, we played very very well and got the result we deserved.
“I cannot remember going away from home in the Premier League and dominating like that.”