The Ivorian scored twice in the second half to finally give the away side the lead it needed in a match it controlled against Alan Pardew's team at the Sports Direct Arena.
City was on top throughout but had to fend off one or two dangerous Newcastle counterattacks, with Joe Hart denying Hatem Ben Arfa in the first half.
David Silva and Gareth Barry had already gone close before the away side finally found the breakthrough when Toure brilliantly curled a shot past Tim Krul after 70 minutes.
The Ivorian midfielder then converted from close range as City took advantage of Newcastle's push for an equalizer.
Both managers elected to name unchanged sides following key victories during the week but Alan Pardew did have a change of formation up his sleeve. Papiss Cisse was partnered by Demba Ba in attack as Newcastle reverted to a more orthodox 4-4-2 that left Jonas Gutierrez shifting out from the center of midfield to the left flank.
Having established an effective defensive shield in the opening 10 minutes, City slowly began to grow into the game in an attacking sense. The fluid movement of the front four resulted in Samir Nasri threading a pass through to Silva, whose left-footed shot across goal was palmed away by Krul.
Silva turned creator to lay on a pass for Sergio Aguero, who forced another save out of Krul but it was not until close to the half hour mark that Newcastle had its first sight of goal. Gael Clichy was dispossessed by Ben Arfa, who raced past Joleon Lescott before picking out Ba, but the Senegalese shot just over the crossbar from 25 yards.
The Magpies went closer minutes later. Ben Arfa forced an excellent save from Hart on the volley after Ba's blocked effort had ricocheted into his path.
The two chances undoubtedly lifted the home supporters and Newcastle began to show more energy and movement as an attacking force. City, though, remained threatening and only determined blocks from Fabricio Coloccini and Davide Santon, the latter on the goal line, prevented Barry from opening the scoring with two shots after a Silva cut back.
The second half started much like the first, with Cisse and Ba frustratingly isolated and losing their battle against Lescott and Vincent Kompany. City, while on top, was beginning to show signs of anxiety itself, though, as despite the team's control over the flow of play a first goal continued to elude it.
Toure pushed up into a more attacking role after Nigel de Jong replaced Nasri but it was the Dutch substitute's misplaced touch that handed Newcastle the first half chance of the second frame. Gutierrez escaped down the left and, with the help of Ba, worked the ball across the edge of the penalty area to Ben Arfa, who turned Clichy but thumped his shot over the bar from a tight angle.
That is not to say, however, that Mancini's tactical change did not work. With 20 minutes to play and Edin Dzeko thrown into the fray in search of a goal, Toure worked a neat one-two with Aguero before curling a perfectly placed shot into the bottom corner of Krul's goal from 20 yards.
The goal forced Newcastle to open the game up in search of an equalizer and City came close to putting the game to bed less than five minutes after Toure's opener. Dzeko had already blasted wide before Silva picked out Aguero with an exquisitely chipped through ball only for the Argentine to shoot wide with only Krul to beat.
Cisse headed just wide from substitute Shola Ameobi's cross but Toure went even closer with a header of his own, flicking a cross just wide of Krul's right post.
Toure had an even better chance to close the deal after 83 minutes. Aguero's pass set the Ivorian free but the midfielder slipped at the crucial moment as he rounded Krul. Toure managed to nudge the ball back to Aguero but he couldn't control his shot and missed the target with the goalkeeper stranded.
Micah Richards, added to the defense from the bench, had to make a brilliant block to deny Ameobi before City raced up the field from the resulting corner to seal three points. Aguero rushed down the right side before switching the ball across to Clichy and the Frenchman was able to pick out Toure in the box, where he made no mistake from close range.
Hart had to deny Ba and Ameobi before referee Howard Webb called a halt to proceedings to send City three points clear at the top of the table ahead of Manchester United's clash with Swansea City later on Sunday.
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