Joey Barton's 52nd minute goal gave Manchester City their victory, leaving the sad Trotters without a win in seven games.
The run has seen Wanderers slip from fourth in the table to the bottom half.
Manager Sam Allardyce have done some surgery before the game, making four changes and dropping former Real Madrid players Ivan Campo and Fernando Hierro to the subs bench.
But after a sterile first half by both sides, Barton took the game's only clear cut chance to inflict more misery on the home side.
Wanderers started the game with something of a new-look back four.
With Nicky Hunt suspended and Rahdi Jaidi injured, Bruno N'Gotty was switched from full-back to his more usual central defensive role along side newcomer Tal Ben Haim.
That left Anthony Barness and Julio Cesar in the full-back places while Kevin Nolan was brought in for Ivan Campo.
City brought back Nicolas Anelka in place of Jonathan Macken, who was named as one of the substitutes.
Recent results made it fairly predictable that both sides would make something of a cautious start to the game.
Wanderers just about had the edge of the opening exchanged with Jay-Jay Okocha putting a long-range shot just wide of the target, while Barness should probably have done better with a half-volley from the edge of the area.
Yet it was City who provided the first real threat, neat approach work setting up Robbie Fowler to bring a good save from Jussi Jaaskelainen in the Bolton goal.
That brought some life into Wanderers' attacking play and David James was forced into an instinctive effort to keep out of fierce shot from Barness.
If the first half had been dull, the second half started a goal out of the blue.
City, having caught pace with Wanderers' early charge, suddenly burst into life to score the opener in the 52nd minute.
Fowler and Anelka both got clear of the markers and when the ball has slipped into the area Barton ran clear to score.
Wanderers' reaction was to bring off captain Okocha and introduce 18-year-old Portuguese striker Ricardo Vaz Te, scorer of 18 goals in the reserves of this season.
He quickly made his mark in a flowing move that started and finished with Ben Haim, but the Israeli could not finish, as he mis-kicked in front of goal.
Les Ferdinand was brought into the action in the 75th minute and responded by forcing James into a good save, but City looked comfortable as they soaked up everything Wanderers had to offer although speed was unlucky to see his fierce shot whistle past a post.
Man of the Match: Sylvain Distin - The City captain was in total control at the heart of the defence to give his side a solid platform for the victory.