The comfortable win for City against a toothless Villarreal, who were missing both first-choice strikers, lifted them above Napoli into second in Group A on seven points, three behind Bayern Munich after the Germans beat the Italians 3-2.
Napoli are two behind City, while La Liga strugglers Villarreal are out of contention having lost all four games.
"We know that in the Champions League everything can happen," City's Italian coach Roberto Mancini, who needed an ice pack on his head after colliding with the dugout roof, told ITV.
"My head is sore... I did the same thing here five years ago," he joked. "But we are going well and want to improve if possible."
Ivory Coast midfielder Toure, who played for Villarreal's La Liga rivals Barcelona before joining City, opened the scoring in the 30th minute at the Madrigal when he picked up a David Silva pass and shot low past goalkeeper Diego Lopez.
The rangy Toure used his strength to weave through the Villarreal defence for his second and the Premier League leaders' third with around 20 minutes left, prompting the home fans to begin heading for the exits.
Silva, who used to play for Villarreal's more illustrious local rivals Valencia, provided the main spark of quality for City in a dominant performance by Mancini's side.
Villarreal have been hit by a string of injuries and were lacking any kind of goal threat with first-choice strikers Italy's Giuseppe Rossi and Nilmar of Brazil both absent.
"I don't think we can criticise anyone," midfielder Borja Valero told reporters.
"All those who don't play much or have come in from the youth side did what they had to do," he added. "They [City] are a very strong team and we did what we could."
Valero said it would be tough overhauling Napoli to clinch third place and a berth in the Europa League, Europe's second-tier club competition.
"While there is life there is hope and even though the goal is a difficult one we'll try to get there."
