Speed fired past debut Villa keeper Gabor Kiraly
A 75th-minute penalty from Gary Speed helped Bolton snatch the points against the run of play at Villa Park.
Speed converted from the spot after Nicolas Anelka had been bundled down inside the box by Stilian Petrov.
The visitors had goalkeeper Jussi Jaaskelainen to thank after a string of brilliant saves denied the home side.
Craig Gardner and Chris Sutton had the best chances for Villa in the second half, but neither man could not find a way past Jaaskelainen.
The result was harsh on Villa, who produced plenty of chances in both the first and second half.
Gabriel Agbonlahor was a constant threat to Bolton on the right flank - and it was the winger who created the first clear-cut chance for Villa in the first half.
His incisive cross sparked a goalmouth scramble and Abdoulaye Meite was forced to clear after Sutton's shot was blocked on the line.
The England Under-21 international again used his ample pace to collect a brilliant defence-splitting pass from Liam Ridgewell, but his acute shot agonisingly curled across the face of goal on 30 minutes.
The home side should have taken the lead five minutes after half time.
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Agbonlahor's well-directed header found Craig Gardner unmarked inside the six-yard box, but his shot was well saved by Jaaskelainen.
The Finnish keeper again came to Bolton's rescue when he brilliantly tipped Gary Cahill's powerful 30-yard strike past his left post on 66 minutes.
Agbonlahor once again had the home fans on their feet when he raced past Henrik Pedersen into the Bolton box, but Jaaskelainen forced the winger to shoot wide into the side netting on 72 minutes.
But the complexion of the game came when referee Mark Clattenburg pointed to the spot after Petrov bundled over Anelka in the box.
Speed smashed the penalty right down the middle of debut Villa keeper's Gabor Kiraly's goal, much to the delight the travelling away fans.
Villa frantically pushed forward in hope of finding an equaliser. Substitute Angel cut through the Bolton defence but shot just wide of Jaaskelainen's post.
The Finn was in the thick of the action once more, this time diving low to save Petrov's drive from the edge of the box.
And Sutton's flick from a Gardner shot in the dying minutes just went wide.
Villa boss Martin O'Neill on referee Mark Clattenburg's decision to award the penalty:
"I have seen it and I think it was particularly harsh.
"I think (Nicolas) Anelka struck the back of Stilian Petrov's leg, but we didn't have the luck today.
"We should have won the game, no argument. We should have won the game by a good distance.
"We were thrusting forward at every opportunity. The effort we put in and the football we played was an absolute delight."
Bolton boss Sam Allardyce:
"We were a bit fortunate at times but you have to give the players credit for the way they defended today.
"There was a poor miss by Villa in the second half - that's where you pay the price in the Premiership."
"We have faltered in the past but this time it may not be the case.
"The teams around us are all ones still in Europe, so that may tell on them this time, but we need to avoid injuries to key players."
Aston Villa: Kiraly, Mellberg, Cahill, Ridgewell, Barry, McCann (Gardner 46), Petrov, Davis, Agbonlahor, Baros (Angel 71), Sutton.
Subs Not Used: Olejnik, Bouma, Hughes.
Bolton: Jaaskelainen, Hunt, Meite (Ben Haim 67), Faye, Campo,Nolan, Speed, Anelka, Pedersen, Davies, Giannakopoulos (Tal 29), Tal (Gardner 57).
Subs Not Used: Al Habsi, Vaz Te.
Booked: Faye, Davies, Pedersen, Gardner.
Goals: Speed 75 pen. Att: 27,450 Ref: M Clattenburg (Co Durham).