Villa appeared set to hold on for a point after resisting almost constant City pressure in the second half, but Toure struck with a clinical left-foot shot to break the deadlock after 82 minutes with his first league goal this season.
Home keeper Brad Guzan had made several saves to keep City out but he was powerless as Villa's defence finally buckled.
Aguero's snap shot after 88 minutes wrapped up the victory which moved City into second place with 14 points from seven matches, two behind Chelsea who host Arsenal on Sunday.
(Writing by Martyn Herman; Editing by Ken Ferris)
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