Villa broke the deadlock through Stephen Warnock after 61 minutes but were rocked by two goals in two minutes from Martin Petrov, with a penalty, and David Ngog.
The Trotters climbed above Blackburn into 18th spot, three points behind Villa and with a match in hand.
Angry Villa fans called for Alex McLeish to be sacked during the final stages of the game.
But the home side were made to pay for not cashing in on their first half dominance when veteran striker Emile Heskey was a constant threat.
Defeat means it is officially Villa's worst home season in their history with only four wins compared to six in 1994-95 and 2004-2005.
They have won only one of their last 13 league games and are in the middle of the fight to stay up along with the likes of QPR, Wigan, Blackburn and Bolton.
Bolton survived the first half onslaught, with defender Tim Ream impressing, and looked more of a threat after the break with Mark Davies influential in midfield.
Villa, with five academy products in their side, made a positive start and could have gone ahead inside the first minute after Marc Albrighton won a corner.
Charles N'Zogbia's centre picked out Chris Herd who headed inches over the bar.
Indecision in the Wanderers back four almost set up a chance for Heskey who half-volleyed over the bar at full stretch.
Former Villa midfielder Nigel Reo-Coker made a timely tackle to halt a dangerous run from Albrighton into the Bolton box.
Bolton came more into the game and Nathan Baker blocked a shot from Chris Eagles after he exchanged passes with Ryo Miyaichi.
A flick from Heskey almost played in Andreas Weimann but Bolton keeper Adam Bogdan reacted quickly to clear from the edge of the box.
Heskey was looking impressive and forced Bogdan to save away to his left with a shot on the turn.
Bolton boss Owen Coyle and Villa coach Kevin MacDonald had to be kept apart by fourth official Craig Pawson after Miyaichi was bundled into touch by Villa full-back Eric Lichaj.
Miyaichi was quickly back on his feet and tested Villa keeper Shay Given with a low drive.
But Villa were soon back on the offensive and Heskey stung the palms of Bogdan after more good play.
Bolton defender Samuel Ricketts became the first player to be booked after 35 minutes for bringing down Albrighton.
Warnock was denied by the woodwork after 38 minutes when his 15-yard drive rattled the crossbar after he had been teed up by Albrighton.
Then N'Zogbia clipped the outside of a post with a 30 yard free-kick on the stroke of half-time.
Coyle made a half-time substitution with striker Kevin Davies replacing Miyaichi.
But Given had to be alert to parry away a dipping 35 yard free-kick from Eagles.
After 61 minutes Warnock broke the deadlock when he turned home a right wing cross from N'Zogbia.
Bolton retaliated and stung the home side by netting twice in two minutes to go in front.
Petrov levelled from the penalty spot within 60 seconds after Carlos Cuellar was adjudged to have brought down Mark Davies.
Then Eagles had the time and space to pick out Ngog who made no mistake from eight yards out.
Bolton defender Ream was booked for dissent as Villa tried to retaliate.
But N'Zogbia shot high and wide and a dangerous cross from the winger eluded everyone as Bolton coped quite comfortably in the final 20 minutes.
Lichaj was booked for disputing a throw-in in injury-time.
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