The mercurial Italian, again in the headlines for non-footballing reasons on Saturday morning, spurned a hatful of chances but eventually got on the scoresheet in another commanding City display at the Etihad Stadium.
Balotelli might have had a hat-trick before City took the lead with a Gretar Steinsson own goal in the 23rd minute but made sure of victory in the 69th minute.
City's win was a record-equalling 19th in succession at home in the Premier League and it left Bolton deep in relegation trouble.
There were suggestions Balotelli might have been dropped following reports he had been on a night out in Liverpool in breach of a club curfew into the early hours of Friday.
Roberto Mancini not only retained him in his starting line-up but deployed him as a lone striker while Sergio Aguero, Edin Dzeko and David Silva were left on the bench.
Balotelli responded with a display of pace and vigour that might have yielded several goals before he finally struck.
Bolton had attempted to curb City by fielding a defensive side, bringing in an extra centre-back in Zat Knight and pushing Tim Ream forward in a 4-1-4-1 formation.
Yet they were in trouble right from the start as City went straight on the offensive.
Samir Nasri had a great chance with just a minute gone as Pablo Zabaleta pulled the ball back but the Frenchman did not shoot first time and David Wheater blocked.
Balotelli was also quickly in the action and went even closer as he struck the post from a tight angle from a Yaya Toure pass just a minute later.
Nasri pounced on the rebound but Adam Bogdan recovered to make a fine reaction save and Steinsson cleared.
Balotelli had another great chance soon after as Adam Johnson combined with Zabaleta on the right and crossed low but the striker, who did well to reach the ball, turned and shot wide.
Balotelli might even have had a hat-trick by the 13th minute as he found himself onside and in the clear but blazed over.
City suffered a blow when Zabaleta was forced off injured in the 19th minute and Kolo Toure took his place at right-back.
City's opener eventually came from an unlikely source as a speculative long-range effort from Gael Clichy took a deflection off Steinsson and beat Bogdan at the near post.
Balotelli then fired a free-kick over and missed with another effort before the magnificent Yaya Toure also saw an attempt drift wide as City maintained the momentum.
Bolton made a rare attack after half an hour as Nigel Reo-Coker got forward and whipped over a cross but David Ngog was unable to connect.
Ngog had a better opportunity moments later but Joe Hart stood tall to save.
Ryo Miyaichi then pounced on a Kolo Toure error to aim a shot at the bottom corner but Hart produced a fine fingertip save.
Balotelli appealed for a penalty after tangling with Knight but Mark Clattenburg gave nothing.
Kolo Toure went close but shot straight at Bogdan, who then denied Balotelli with his feet just before the break.
Balotelli spurned another gilt-edged chance within a minute of the restart as Gareth Barry presented him with a one-on-one with Bogdan with a superb defence-splitting pass.
Bogdan was alert to the situation and spread himself to save as Balotelli set himself.
Barry had a sight of goal himself but shot well over while Balotelli had another appeal for a penalty rejected on the edge of the area.
Kolo Toure burst forward and exchanged passes with Nasri before shooting across goal.
City's tempo then dropped but they almost benefited from a second own goal as, in trying to dispossess substitute Dzeko, Darren Pratley managed to shoot against his own crossbar.
City finally doubled their lead and Balotelli at last - and deservedly - got on the scoresheet with 21 minutes remaining.
Johnson was the provider as he weaved through the defence to set up Balotelli from close range with a nifty backheel which squeezed between Bogdan and Wheater.
Dzeko chipped forward to give Johnson a shooting chance but the winger shot wide.
Yaya Toure instigated another attack with a driving run but Nasri saw his shot blocked.
James Milner then came on for Nasri as City wound down the clock towards another victory.