Toure netted his third goal in two games with his header 17 minutes from full-time after the hosts had threatened to become the second team to take a point off City.
Jay Bothroyd had given QPR the lead in the first half before Edin Dzeko and David Silva replied either side of the interval.
Neil Warnock's team levelled when Heidar Helguson deflected home from close-range but Ivory Coast midfielder Toure had the last word to keep City ahead of Manchester United going into the international break.
QPR were without Adel Taarabt following a stomach bug but Shaun Wright-Phillips and Joey Barton impressed against their former club.
City manager Roberto Mancini made six changes to their starting line-up despite a convincing Champions League victory over Villarreal in midweek, when Toure had netted twice.
Sergio Aguero and Dzeko were among those restored to the team, while Silva recovered from a back suffered during the end of the win in Spain.
The match started with the same intensity of the previous game at Loftus Road when Warnock's side defeated Chelsea during a controversial clash.
Helguson, who scored the winner that day against Chelsea, had a couple of early efforts on goal from the edge of the area but one went wide and other was saved by Joe Hart.
He went close again midway through the first half when the striker climbed above Micah Richards and met Barton's corner, with his effort looping just wide.
Gareth Barry had City's first effort on goal in the opening minute but his drive flew over the crossbar, but clear-cut opportunities proved difficult to create for the visitors.
They were behind just before the half-hour mark after Bothroyd was tripped on the touchline by Aleksandar Kolarov, although replays suggested it was a harsh decision.
Barton swung over the free-kick and Bothroyd got between Stefan Savic and Richards before planting his header into the bottom corner, his second in as many games.
It was the first time City had been behind in a Premier League game this season. And they could have been further behind when Jamie Mackie's powerful volley tested Hart.
City responded by stepping up the pace of their attacks, with Paddy Kenny saving with his feet to deny Aguero.
The equaliser came two minutes before the break, with a move starting when Barry slipped the ball to Dzeko on the left flank.
Bosnia striker Dzeko cut inside, around Anton Ferdinand, and powerfully finished into the bottom corner.
They were ahead seven minutes after the break through a moment of class from Silva.
Dzeko carried the ball down the left flank and when the cross came over Silva looked ready to lay the ball back to a team-mate.
But the Spain midfielder turned sharply - tricking Ferdinand and Danny Gabbidon - before driving into the bottom corner beyond Kenny.
Dzeko should have added another but went just wide with another effort, while Kenny also saved another shot from the striker and Aguero went just wide.
The game took another twist 22 minutes from full-time when the hosts levelled.
Armand Traore crossed from the left and Bothroyd's diving header went in off Helguson's back, with the goal standing despite City protesting for offside.
But City responded five minutes later when Toure headed home powerfully from Kolarov's cross.
Source: AFP
Source: AFP