However, Raheem Sterling made Premier League history by scoring in his sixth successive match against the Cherries to restore their lead, before Ilkay Gundogan wrapped up the points 11 minutes from time.
City, who extend their unbeaten start to 14 matches and have now won all eight of their home league games this season, will now enjoy their five-point lead until at least Sunday, when closest challengers Liverpool host Everton in the Merseyside derby.
Pep Guardiola was without injured Premier League top-scorer Sergio Aguero due to a muscle problem, while David Silva was also left out of the starting lineup as the home side made five changes from the midweek Champions League draw with Lyon.
It did not stop City from making another quick start, though, with Leroy Sane's pace causing Bournemouth numerous problems in the opening exchanges and Gabriel Jesus almost turning a wicked delivery from Oleksandr Zinchenko past Asmir Begovic.
Zinchenko was involved again when City took the lead after 16 minutes as Sane beat a hesitant Begovic to his clipped pass over the defence, and although the Bournemouth keeper thwarted the initial effort, Bernardo was the quickest to react to the loose ball inside the area and fired a confident first-time finish into the empty net.
The hosts were immediately back on the front foot after the restart as Sane once again broke in behind the defence before this time pulling a cross back for Bernardo, whose first-time volley was blocked before it could test the keeper.
City continued to dominate as the first half wore on, but Bournemouth did well to prevent Guardiola's side from creating many clear-cut chances and the closest they came in the remainder of the first half saw Sane blast a powerful effort way over the crossbar.
Indeed, it was Bournemouth who ended the half on top and they came close on a couple of occasions before their equaliser, with Wilson almost getting on the end of Joshua King's cross and Nicolas Otamendi blocking an effort from King before it could test Ederson.
The visitors' increased pressure paid off right on the stroke of half time when Simon Francis hoisted a cross into the box which Wilson met with a brilliant header, diverting the ball past Ederson and into the far corner.
It was a perfect end to the first half for Bournemouth, and they threatened a similar start to the second too as King lofted a cross towards the back post which dropped narrowly wide of the target and just short of Charlie Daniels.
City soon began to increase their pressure again, though, and the hitherto quiet Sterling almost restored their lead in spectacular fashion when he embarked on a mazy run which saw him escape the attention of numerous defenders before seeing his eventual effort deflect against the post.
Sterling's moment did come shortly before the hour mark, though, with the in-form winger firing a rebound into the roof of the net after Begovic had parried Danilo's low strike back into a dangerous area.
The goal saw Sterling become the first player in Premier League history to score in his first six matches against a particular club and took his overall tally against Bournemouth to eight goals and two assists in just six appearances.
Bournemouth's first-half equaliser suggested that City may need a two-goal cushion to make sure of the points, and they almost got it when Jesus fashioned a clever backward header towards the bottom corner which Begovic needed to turn around the post.
The resulting corner eventually saw Jesus beat his man on the byline and pull a low cross into the box for Fernandinho, who drilled his effort wide of the far post when he should have done better.
Guardiola turned to David Silva off the bench in an attempt to make sure of the points, and the Spanish playmaker had an immediate impact when he slid a pass through for Sane, who sent another low cross into the middle which was this time stroked home by Gundogan.
Sane deserved a goal for his individual performance and almost capped off the scoring late on when he turned Steve Cook inside out before seeing his powerful drive turned over the crossbar by Begovic.
The result means that City are now unbeaten in their last 20 Premier League games, whereas Bournemouth have lost four games in a row for the first time since September 2017.
MAN CITY (4-3-3): Ederson; Danilo, Laporte, Otamendi, Zinchenko (Delph 54'); Fernandinho, Gundogan, Bernardo (Mahrez 87'); Sane, Sterling, Jesus (Silva 77')
BOURNEMOUTH (3-4-3): Begovic; S Cook, Minga, Ake; Francis, L Cook, Surman, Daniels; King (Stanislas 85'), Wilson (Mousset 85'), Fraser (Brooks 72')