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."
TOUGH GOAL
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.
Italy striker Mario Balotelli, returning from a three-match European ban, doubled the visitors lead with a penalty in first half stoppage-time after he was felled in the area by Mateo Musacchio, calmly tucking away the spot-kick for his seventh goal in seven matches in all competitions.
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.
Three points from their away trip to Napoli on November 22 will guarantee City a place in the knockout rounds. Their final game is at home to Bayern on December 7.
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.
The Spain playmaker, who helped the Iberian nation to their first World Cup triumph in South Africa last year, was given a rousing ovation from the home fans when he was replaced by Adam Johnson in the second half.
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.
Coach Juan Carlos Garrido was forced to call up a number of youth players and started with 20-year-old Joselu, current top scorer in the Spanish second division with Villarreal B, alone up front.
"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."
