The away side were gifted the perfect start when Richard Stearman headed the ball into his own net in the first minute.
The game looked to be done and dusted until Kevin Foley struck to give the hosts hope. Hope soon turned into genuine belief when substitute Steven Fletcher headed a second to set up a dramatic finish.
A header from Steven Mouyokolo in the dying moments was inches away from levelling the scores and completing a dramatic comeback for Wolves.
This win has seen Bolton climb to fifth in the table, with a place in the Europa League very much in their sights.
Wolves, however, have a relegation battle on their hands, as they sit second from bottom, level on points with West Ham who prop up the table.
The game was 51 seconds old when Bolton took the lead. Lee whipped in a cross from the right wing and with Matthew Taylor breathing down his neck, Stearman sent a flying header past Marcus Hahnemann and into the back of his own net.
Wolves refused to let their nightmare start unsettle their game plan and they swept up field with retaliatory intent.
The Molineux faithful watched a physical battle unfold at a furious pace. Neither side afforded their opponent a moment's peace, which resulted in a frantic tussle lacking cutting edge in the final third.
McCarthy's troops dominated possession, but looked susceptible to the visitors' counter attack. In the final 10 minutes of the first half, Wolves started to find gaps in Wanderers' rearguard.
First the mischievous left foot of Nenad Milijas propelled a wickedly swirling free kick over the Bolton wall and towards the bottom right hand corner, but Jussi Jasskelainen was equal to it beating it out to his right.
The rebound fell to Kevin Foley, who stood a cross up at the back post to Sylvan Ebanks-Blake and the striker showed mercy with a woeful volley into the stands.
Milijas was at it again as he cut in from the right and catapulted another devilish left footed drive at goal. Once again Jasskelainen had the measure of it as he palmed it around the post.
A misguided header from Elmander let Wolves off the hook, before Matthew Jarvis was foiled by the body of Bolton's Finnish goalkeeper.
Milijas picked up from where he left off in the first half and hit the bar inside three minutes of the restart.
Jarvis picked out the number 20 on the edge of the box and the Serbian midfielder dug out a shot that flew over the Jasskelainen and clipped the woodwork.
The big Swede received a pass from Holden in the box. Surrounded by a battalion of would-be tacklers there seemed nothing on, but the striker left them dumbfounded as he span through their challenges and placed a precise shot past Hahnemann.
Minutes later provider turned scorer. Kevin Davies slipped a pass inside George Elokobi for a galloping Lee, who opted to lay the ball into Holden as Hahnemann dived at his feet. The American midfielder swept the ball into the empty net.
As Bolton patted themselves on the back for a job well done the hosts pulled a goal back. Jarvis burst inside from the left wing and laid the ball into Foley who bent a curling shot into the right hand corner.
With just over 10 minutes to play Jarvis got his second assist of the day, sending a corner over the flapping Jaaskelainen to Fletcher lurking at the back post. The Scottish striker stooped to head Wolves right back into the game.
Mouyokolo was a whisker away from being a hero when he rose to meet a cross from Jarvis and headed goalwards.
The crowd held their breath as the ball sailed agonisingly wide of the right hand post.