Thomas Hitzlsperger's goal two minutes from time earned Aston Villa their first away win of the season.
The German's strike also meant a first home defeat of the season for a Bolton side that had earlier looked set to take all three points.
El Hadji Diouf gave Wanderers the lead in the 21st minute, but then saw Gavin McCann wipe that out just before the break.
In the early stages Diouf headed against a post and Villa keeper Thomas Sorensen saved from Kevin Davies while at the other end Juan Pablo Angel almost gave Villa an early lead.
Diouf and Gary Speed managed to get shots on target but neither had the power or accuracy to test Sorensen.
Bolton deservedly took the lead in the 21st minute. Kevin Nolan played a searching diagonal ball into the six-yard box where Diouf managed to get in front of the Villa defence and stretch out a foot to deflect the ball past Sorensen.
Ricardo Gardner was booked in the 23rd minute for a foul on Nolberto Solano and was lucky to escape a red card nine minutes later when he brought down McCann. Referee Andy D'Urso merely lectured the Jamaican international.
However Villa were level four minutes before half-time as McCann rose above Gardner to head home Lee Hendrie's cross at the far post.
On the balance of play it was no more than Villa deserved but they were fortunate not to concede shortly afterwards as Sorensen reacted quickly to beat Diouf to the ball.
Gary Speed has still not scored for Wanderers following his move from Newcastle United in the summer, but should have done better with two chances early in the second half.
He was only inches away from getting the final touch with the first chance and only succeeded in hitting the second opportunity over the bar.
After more Bolton pressure Speed managed to knock the ball down to Pedersen, but Sorensen was aware of the danger.
Pedersen then fired a shot just over the bar for Sam Allardyce's side while for Villa Hendrie saw his effort saved by Andy Oakes after Carlton Cole had created the opening.
Angel then danced around four defenders only for Solano to waste the chance and then the Colombian saw another opportunity fly over the bar.
Nolan was not too far away from scoring with a header but then Villa handed Bolton a reminder of their attacking prowess when Cole headed narrowly over the bar.
Diouf went close to grabbing his second goal of the game when he headed Nolan's cross on to the post as both sides set up a grandstand finish.
And it was Villa who grabbed the spoils thanks to Hitzlsperger.
MAN OF THE MATCH: El Hadji Diouf (Bolton) - Scored one goal, hit the post later on and was a threat to the Villa defence throughout the 90 minutes.