The hosts dominated the opening period but shot themselves in the foot - as they had in their previous game - by conceding a goal in the first minute, Richard Stearman heading past his own goalkeeper Marcus Hahnemann.
Second-half strikes from Johan Elmander and Stuart Holden gave Bolton a 3-0 lead, and although Kevin Foley and Steven Fletcher swiftly reduced the deficit, Mick McCarthy's side were unable to find the equaliser.
While the visitors will be delighted to have held out to keep their impressive form going, McCarthy's side remain in the Barclays Premier League's bottom three.
They have earned plaudits for their football over the last few weeks, but have taken only nine points from 13 league fixtures and results need to improve fast.
Wolves had caused Arsenal plenty of problems on Wednesday night in one of a string of creditable performances they have put in recently against top-four sides, but made life difficult for themselves from the off in that match by conceding a goal almost immediately after kick-off.
It seemed they had learned little from the experience as they again fell a goal behind only a few seconds in against the Trotters.
Lee Chung-yong's cross from the right was only partially cleared and the South Korea winger headed the ball straight back into the danger zone where Stearman, under pressure from Matt Taylor, nodded it past Hahnemann and into the net.
It was a disastrous start, but the hosts tried to rally quickly and their skipper Karl Henry forced a save out of Jussi Jaaskelainen with a lofted delivery. From the resulting corner, Matt Jarvis teed up Nenad Milijas, whose drive was blocked.
Moments later Sylvan Ebanks-Blake brought down Stephen Hunt's cross and protested that Gary Cahill pulled him back as he shaped to shoot, but referee Peter Walton ruled that the Wolves striker controlled the ball with an arm.
Kevin Davies then saw a shot saved by Hahnemann, before Ebanks-Blake hit the post at the other end - although replays suggested he had used his hand.
Wolves went the closest yet to making it 1-1 when Milijas rifled a free-kick at goal which Jaaskelainen did well to parry. The ball fell to Foley, whose floated cross was volleyed over the bar by Ebanks-Blake.
Milijas called Jaaskelainen into action again a minute before the break with a swerving shot and Bolton survived a scramble that followed shortly after.
Jarvis then broke into the box but was thwarted by the Finnish stopper.
Wolves' hunt for a leveller showed no signs of letting up as the second half got under way, with Milijas unlucky once more after his chip from the edge of the box clipped the bar.
Bolton attempted to wrestle back possession and Elmander was beaten to Davies' flick-on by Hahnemann.
The Swedish striker then laid the ball square to Fabrice Muamba, whose shot was deflected wide.
Jarvis, tipped to be in the England squad announced after the game, sent an inviting ball into the Bolton box but a handful of his team-mates had all run too soon and it drifted behind them.
The hosts looked to be in the ascendancy, but just after the hour mark, they were undone by a moment of magic.
Holden, who had brought a save out of Hahnemann moments earlier, played the ball in to Elmander, who had his back to goal but twisted and turned around a crowd of defenders before calmly finishing in the bottom corner.
Holden then got on the scoresheet himself, slotting Lee's pass into the net and Wolves looked dead and buried.
They swiftly pulled on back, though, as Foley collected the ball from Jarvis and angled it past Jaaskelainen.
Suddenly Wolves' tails were up and after piling on the pressure for 10 minutes, they grabbed another.
Jarvis was again the provider, sending in a corner which Jaaskelainen flapped a glove at but missed, allowing substitute Fletcher to nod the ball over the line.
The comeback appeared to be on, but nobody could get on the end of crosses from George Elokobi and Fletcher in the closing stages and Steven Mouyokolo glanced wide right at the end as Bolton made off with the win.