Club captain Kevin Davies steered Bolton closer to safety as he took his goal tally into double figures for only the second time since moving to the Reebok Stadium.
The industrious striker made it 10 for the season in the 11th minute and his side appeared to be coasting after Matt Taylor's goal two minutes earlier.
However, West Ham stormed back and Scott Parker gave them hope with a close-range finish but they were unable to claim the point that their possession perhaps deserved.
Bolton made the breakthrough following a splendid free-kick from Taylor.
He curled his effort into the corner from 20 yards after Jack Collison had been penalised for a challenge on Mark Davies.
The Hammers were left catching their breath again two minutes later when Bolton extended their lead.
Johan Elmander, back in the side after a four-match abscence with a hamstring injury, showed neat footwork to carve out an opening for Davies.
He took advantage to sweep the ball home and Bolton looked almost home and dry at that early stage.
There was more misery for the visitors in the 15th minute when James Collins was stretchered off with what appeared to be a hamstring injury. He was replaced by James Tomkins.
West Ham were anxious to get back in the game before half-time and David Di Michele found space at the back post 14 minutes later but dragged his effort wide.
They launched a swift counter-atack seven minutes afterwards when Carlton Cole released Mark Noble with a delightful through ball.
Noble was clear on goal but instead opted to try to find a team-mate. It proved to be the wrong call as Gary Cahill was able to make the clearance with a degree of comfort.
Then Di Michele scampered clear and drew Jussi Jasskelainen out of his goal but his finish was dreadful, the ball missing the target by a distance.
The Hammers kept up the pressure and Cole got into a good position in the penalty area but his effort failed to trouble Jaaskelainen.
West Ham almost pulled a goal back two minutes into the second half when Taylor cleared Cole's effort off the line after Tomkins had headed the ball on.
Bolton hit back and Taylor tested Green after Jlloyd Samuel had launched the ball forward.
West Ham got their reward in the 66th minute when Parker scored after timing his run to perfection to get on the end of a cross from Jonathon Spector.
It was no more than the visitors deserved for the work they had put in after conceding two goals in the first 11 minutes. Now it was Bolton's turn to look vunerable.
West Ham maintained the momentum and Cahill cleared off the line from Di Michele's effort.
There was another scare for Bolton in the 82nd minute when Jaaskelainen spilled a header from Cole, only to recover just in time.
West Ham were running the show but ran out of time and slumped to their first defeat on the road in the Barclays Premier League in eight games.
It was little wonder manager Gianfranco Zola looked a picture of bewilderment at the end of the game.