Wanderers' six-match unbeaten run at the Reebok came to an end as substitute Sulley Muntari netted an injury-time winner for the Black Cats.
Ivan Klasnic looked to have rescued a point for Bolton after also coming off the bench to make it 1-1 on 87 minutes.
Sunderland had earlier taken the lead on the stroke of half-time in controversial circumstances through Bolo Zenden, with the officials not awarding a foul on Chung-Yong Lee in the build-up.
Wanderers looked to be the team in the ascendency as the game approached its latter stages, particularly when Phil Bardsley produced one of the clearances of the season to deny Kevin Davies just after Bolton had restored parity.
But Sunderland made the most of Bolton's attacking mentality, with Muntari's fresh legs proving decisive as the Whites ventured forward late on in search of the winner themselves.
Whilst Sunderland had been hampered by severe injury problems in the build-up to the game, it was contrasting fortunes for Owen Coyle, who had Daniel Sturridge and Gretar Steinsson back available for selection following respective ankle and knee problems. The pair were restored to starting line-up as the Bolton boss made five changes to the team that was named at Ewood Park the previous week.
One of the Sunderland absentees was captain Lee Cattermole, so it was Bolo Zenden who took up possession of the armband. The Dutch playmaker was the first player to have an effort at goal, with his free-kick from the edge of the area flying over the crossbar early on.
It was the visitors who bossed proceedings inside the opening ten minutes as they won a succession of free-kicks and corners in and around the Bolton box. They also felt that they should have been awarded a penalty when Ahmed El Mohammady took a tumble under a Zat Knight challenge but referee Kevin Friend correctly waved away any appeals.
Mr Friend was proving pretty consistent with his decision making as again he turned down protests for a spot-kick on 20 minutes. This time, however, it was at the opposite end of the field, with Sturridge going to ground innocuously in a tussle with John Mensah. Replays suggested that the Ghanaian defender clipped Sturridge's heels but it was more accidental than intentional.
By this time, Wanderers could have been occupying a one-goal lead if it hadn't been for a brilliant low save by Simon Mignolet. Just moments prior to the penalty appeal, a well-worked team move from right to left culminated in Kevin Davies playing a clever reverse pass to Matt Taylor. But when the midfielder pulled the trigger, Sunderland's Belgian keeper dived low to his right to turn the ball behind for a corner.
After Taylor's effort, Bolton began to grow into the game and they created a number of decent openings to nudge themselves ahead before the half way was out.
Sturridge and Chung-Yong Lee saw efforts blocked inside the six-yard box, Elmander's near post header missed the target by a couple of yards and Sturridge, again, saw a curler from the edge of the box flick-up off Anton Ferdinand and strike the top of the crossbar.
But just as the fourth official announced that there would be one minute of stoppage time, Zenden broke through the middle of the park to round Jaaskelainen and put Sunderland into the lead.
The Bolton defenders appealed for offside against the former Chelsea and Middlesbrough man, but they fell on deaf ears and it was the Black Cats who went into the interval occupying the lead.
As a response, Owen Coyle made one substitution at the break as Ricardo Gardner was introduced in a straight swap for Fabrice Muamba in central midfield.
The Jamaican had an immediate impact as it was his surging run through the middle of park which presented Sturridge with an opportunity to level the scores five minutes after the restart. Unfortunately, though, the on-loan striker's low curling effort beat Mignolet but not the post, with the ball skimming the outside of the woodwork.
Steinsson fired over from an acute angle, Sturridge saw another effort blocked by a Sunderland body and Chung-Yong Lee volleyed over from eight yards out as Bolton pressed for an equaliser.
Rodrigo and Ivan Klasnic were thrown on with just under 20 minutes left, replacing Taylor and Chung-Yong Lee in the wide areas.
And it was the double change which proved to be at the heart of the Wanderers equaliser, which arrived just three minutes shy of the 90.
Sturridge switched play from right, Robinson played a concise pass down the left channel where Rodrigo took one touch before delivering a inviting curling cross to the far post. Ivan Klasnic was the grateful recipient and he nodded a perfectly weighted finish back across goal, beating Mignolet with the ball creeping just inside the post.
It looked like there was only one team going to go on and win the game, especially when in Wanderers next attack Rodrigo again supplied a cross from the left. Kevin Davies slid in to make contact but, amazingly, Bardsley threw his head at the ball to divert it over the bar for a corner.
Such are the fine margins in the Premier League that that unbelievable clearance proved crucial as Sunderland ventured straight up the opposite end of the field to net the late, late winning goal.
Muntari latched onto Sessegnon's ball from midfield and despite being forced wide by Gretar Steinsson, the Ghanaian managed to squeeze his effort back across goal and into the back of the net, via the boot of Zat Knight.
The result was only Bolton's third home loss of the season, following the defeats by Liverpool in October and Chelsea in January.
Wanderers: Jaaskelainen, Steinsson, Knight, Cahill, Robinson, Chung-Yong (Rodrigo 75), Muamba (Gardner 46), Elmander, Taylor (Klasnic 75), Kevin Davies, Sturridge (Subs not used: Bogdan, Wheater, Cohen, Petrov)
Sunderland: Mignolet, Bardsley, Mensah, Zenden, Malbranque (Muntari 84), Henderson, Onouha, Colback, El Mohammady, Sessegnon, Ferdinand (Subs not used: Carson, Riveros, Knott, Noble, Adams, Lynch)