Leroy Lita gave his side a first-half lead with his debut goal, before Chris Eagles equalised with a terrific free-kick on the stroke of half-time.
Marlon King made sure of his side’s second win of the season as he fired home from the penalty spot just after the break.
Lee Clark made just one change to his starting XI with Wade Elliott replacing Peter Lovenkrands on the left hand side of midfield, as the Dane was dropped to the bench.
On a chilly September evening at St. Andrew’s it was Bolton who made the early running.
But having soaked up the pressure, Blues began to impose themselves more on the game and Leroy Lita was unlucky to see his header deflected wide for a corner.
Jack Butland had to be alert to punch Chris Eagles’ deep cross away from the danger zone, before a superb piece of passing play saw Blues take the lead after a quarter of an hour.
A great ball from Wade Elliott to Paul Caddis saw the right-back collect the ball on the edge of box before cutting inside his marker and lay off a perfect pass across the front of the goal, where Leroy Lita was on hand to slam the ball home from four yards out.
Almost immediately Bolton were forced into making a premature change as Keith Andrews was sent on in place of the injured Jay Spearing.
Clark’s side went close to doubling their advantage after 29 minutes when Elliott’s through ball found Burke in a one-on-one with Adam Bogdan, but the Bolton stopper did well to deny the Scottish winger with his feet.
Blues received a let off after 38 minutes when Chris Eagles’ cross found David Ngog. But from just five yards out the Bolton man headed the ball directly at Butland.
Very much against the run of play, Bolton found themselves back in the game after 44 minutes.
Chris Eagles unleashed a fantastic free-kick from a good 30 yards out that left Butland with no chance as it flew into the top corner.
Half-time: Blues 1 Bolton 1
Blues made a change at the break with Irish international Keith Fahey replacing Hayden Mullins.
Less than two minutes after the restart Blues found themselves back in the lead.
Marlon King was brought down in the box by Marcus Alonso and the Blues striker stepped up and sent Bogdan the wrong way from the resultant spot kick.
Blues were running rampant now and Caddis tested Bogdan with a powerful shot from 20 yards out and then Lita shot just wide.
Blues suffered a major blow after 51 minutes when Caddis collapsed to the ground clutching his right shoulder.
There was the disappointing sight of the right-back gingerly leaving the field accompanied by the club doctor. Curtis Davies was sent on in his place.
Owen Coyle made his second and third substitutions of the game on the hour mark when Benik Afobe and Martin Petrov replaced David Ngog and Chung Yong Lee respectively.
Afobe almost made an immediate impact and would have scored had it not been for an excellent save by Butland who dived at his feet.
Not content to rest on their laurels, Blues continued to push on themselves and Elliott curled an effort just wide of the far post.
Clark made his last change of the game after 71 minutes when Nathan Redmond replaced Burke.
With 20 minutes to go, the game was continuing to swing back and forth between the two sides.
Bolton were awarded a free-kick in a dangerous position just outside the Blues box, but fortunately Eagles couldn’t replicate his first-half spot kick and drilled his effort over the bar.
With ten minutes remaining Redmond was denied a goal-of-the-season contender by Bogdan.
The youngster ran some 70 yards with the ball and evaded several challenges before laying the ball off to King. King slid the ball back to him and he curled in an exquisite effort towards the top corner, which the Bolton keeper tipped over at full stretch.
As the game entered its final minutes Bolton continued to press and Butland made a smart diving save to deny Alonso’s well-hit volley and then saved low down from Eagles.
But the Trotters were unable to breach the Blues defence for a second time and Clark’s battlers held on for a deserved victory.
Full-time: Blues 2 Bolton 1
Blues: Jack Butland, Paul Caddis (Curtis Davies, 54), Pablo Ibanez, Steven Caldwell, David Murphy, Chris Burke (Nathan Redmond, 71), Jonathan Spector, Hayden Mullins (Keith Fahey, half-time), Wade Elliott, Marlon King, Leroy Lita.
Subs not used: Colin Doyle, Ravel Morrison, Peter Lovenkrands, Akwasi Asante.
Bookings: Mullins (43).
Goals: Lita (16), King (48, pen).
Bolton: Adam Bogdan, Tyrone Mears, Matt Mills, Zat Knight, Marcos Alonso, Chung-Yong Lee (Martin Petrov, 60), Mark Davies, Jay Spearing (Keith Andrews, 17), Chris Eagles, Kevin Davies, David Ngog (Benik Afobe, 60).
Subs from: Andy Lonergan, Sam Ricketts, Marvin Sordell, Darren Pratley.
Bookings: Zat Knight (36), Mark Davies (40), Chung Yong Lee (45+1).
Goals: Eagles (44).
Attendance: 14, 693
Referee: Carl Boyeson.