Substitute Bafetimbi Gomis looked to have salvaged a point for the hard-working Swans with a ferocious strike in the 89th minute but Toure deflated them with a deflected strike moments later.
Prior to the breathless ending it had been a drab Barclays Premier League contest played in pouring rain, with Wilfried Bony's 26th minute header against his former club looking like it would separate the two sides.
Not for the first time it had seemed a case of City struggling to find top gear after European exertions with Raheem Sterling, the hero of the midweek win over Borussia Monchengladbach, one of the disappointments.
Swansea, who sacked manager Garry Monk in midweek, were excellent in the second half and were it not for the outstanding Joe Hart they may have equalised earlier.
Caretaker boss Alan Curtis and the rest of the bench leapt to their feet as Gomis finally broke through but they were quickly brought back to earth.
City, having named Kevin De Bruyne on the bench, were sluggish throughout even though they controlled the majority of possession.
Their defensive vulnerabilities in the continued absence of captain Vincent Kompany were also exposed again after just five minutes as Wayne Routledge broke through the middle and should have scored
Hart came to City's rescue, blocking with his feet.
It took City 14 minutes to muster an attempt on goal and Bony's tame shot was easily dealt with by Lukasz Fabianski.
A quick Swansea counter-attack saw the visitors create another chance but Hart palmed the impressive Gylfi Sigurdsson's effort over.
Jesus Navas went close at the other end midway through the half as he cut inside to shoot on his left foot
His strike was deflected wide but he picked out an unmarked Bony with his cross from the resulting corner and the Ivorian powered in a header.
It was the fourth time in succession he had scored in this fixture, with two appearances for each club, but he chose not to celebrate, instead pointing to the rain-filled sky.
Swansea might have had a quick reply as Andre Ayew headed over but the first half meandered to a close with only Toure, with a weak shot, threatening again.
Swansea made a lively start to the second period and Sigurdsson was thwarted in front of goal by both Eliaquim Mangala and Hart.
Toure tested Fabianksi from a set-piece before Sigurdsson drew another save from Hart from a free-kick awarded after Bacary Sagna caught Routledge in the head with a high foot.
City, having already sent on Fabian Delph for Sterling at half-time, withdrew David Silva after 68 minutes in the hope De Bruyne could spark them into life.
The Belgian immediately whipped in a dangerous corner but Nicolas Otamendi failed to make clean contact with his header
Delph also threatened with an effort that curled wide.
Still City looked clumsy at the back and Mangala was booked for a poor challenge on substitute Mo Barrow.
They were caught out as Gomis broke through the middle and unleashed a fierce drive which Hart had no chance of keeping out with 89 minutes on the clock.
But joy quickly turned to despair for the Swans as Toure found space out on the right and his curling shot took a deflection and looped over Fabianksi.
Source : PA
Source: PA