It was tough on the hosts who had battled so tirelessly and with keeper Brad Guzan in inspired form and Fabian Delph producing occasional fireworks up front to release the pressure, it seemed the reigning champions would be left frustrated.
But with eight minutes left, Toure conjured up the magic to decide this lively contest, picking up the ball on the edge of the box, waltzing past the legs of three weary defenders before calmly curling the ball inside the post.
With 25 chances created to Villa’s six, few would dispute the result and with Aguero smashing in a second, this victory will go some way to ease the disappointment of the midweek Champions League draw with Roma, along with keeping the heat on Premier League leaders Chelsea.
For all their toil, Villa suffered their third successive defeat (conceded eight and scored none in three games) but they should take heart from a stirring defensive performance for long periods, with the biggest cheer of the afternoon left for Christian Benteke, making his first appearance in the second half for the first time in six months.
City though began this match how they finished – pushing for goals – and only the woodwork denied Aleksandar Kolarov an opener after his deflected shot crashed against the upright via a deflection off Alan Hutton.
Villa weren’t without their chances with Toure having to be at his best to force the marauding Charles N’Zogbia to fire just wide, while Andreas Weimann also proved to be a menace around the box.
As the break approached, the spectacle of a grizzly Manuel Pellegrini on the touchline may have been the inspiration for his toothless attacking force but City could have notched four in the dying minutes of the first period.
Aguero’s glancing header from Kolarov’s curling cross dropped narrowly over, Edin Dzeko blasted high and wide from close range and then the Bosnian striker saw a header hacked away by Aly Cissokho.
It was desperate, heroic and at times fortunate defending by Villa but they held firm and again luck was on their side 100 seconds after the break as Aguero blasted against the post.
The start to the second half was breathless at both ends and Villa broke away immediately as Kieran Richardson’s sloppy first touch denied him a clear shooting opportunity in the box.
City stormed back as Guzan reacted fantastically to palm away Silva’s deflected shot and the Spaniard was at it again, shooting at the keeper after a wonderful weaving run.
With Villa’s players running on empty, it was left for Guzan to keep his side in contention as he shut out Eliaquim Mangala’s header and a tame punt from substitute Frank Lampard.
The impossible seemed perfectly possible on 82 minutes for the hosts, only for Toure to take centre stage and deliver his first goal of the season with Ageuro adding icing to the cake with his late strike.