Bolton, often under-estimated by many people, carved out their belated win after Stiliyan Petrov fouled Nicolas Anelka. Speed dispatched the spot kick past on-loan goalkeeper Gabor Kiraly to plunge Villa to only their second home defeat of the season.
It was a tremendous disappointment for Villa in a game they dominated for long spells but they could have no excuses as they again failed dismally to capitalise upon some good opportunities.
Villa's problems have now come to the surface and they have now gone six games without a win to give manager Martin O'Neill a few headaches.
Bolton, on the other hand, chalked up their second successive win and beating Villa was all the sweeter as it enabled them to move up into fifth place.
They were, however, somewhat fortunate on this occasion as they hardly appeared likely to beat Villa until Petrov's clumsy tackle on Anelka which enabled them to produce their first shot on target in the match.
Bolton's twin striking threat of Anelka and Kevin Davies was non-existent for long spells on this occasion in a scrappy type of game in which neither side hit the high notes.
Villa often mounted the more dangerous attacks but the lack of finishing power was plainly obvious with neither Chris Sutton nor Milan Baros posing any real threat to Abdou Faye and Abdou Meite.
It was a solid no-nonsense performance from Bolton. They never stood on ceremony as highlighted by the fact they had three players - Faye, Davies and Henrik Pedersen - booked in a goalless first half which struggled to come to life.
Often it was a scrambling affair. Petrov and Sutton were involved in one hair-raising incident near the Bolton goal but the Trotters defence managed to prevent Villa getting the ball into the net.
Gabriel Agbonlahor's pace was a problem in patches and the youngster broke clear to get in a shot but the angle was far too tight and he shot wide of the far post, to give a fair idea of the lack-lustre atmosphere surrounding the match.
It could well have been different five minutes into the second half when Craig Gardner, who had replaced the injured Gavin McCann at half-time, somehow managed to screw the ball wide of the Bolton goal from about three yards out following a cross from Gareth Barry.
Another Villa teenager, Gary Cahill, moved up to produce a block-busting shot from 25 yards which Jussi Jaaskelainen tipped over the bar.
But the turning point of the game occurred in the 75th minute when Petrov, under no real pressure, hacked away at Anelka and referee Mark Clattenburg had no hesitation in awarding the penalty which Speed slotted away for only his third goal of the season.