Two goals from the Ivorian and the former Inter striker secured a well needed victory, taking them one step closer to qualification for the last 16
The visitors proved superior throughout the game in an encounter that saw Mario Balotelli net another goal on his return to European action following his three-match ban for his Europa League dismissal against Dynamo Kiev last season.
Roberto Mancini rested the in-form Micah Richards and Sergio Aguero, while Stefan Savic, Samir Nasri and Balotelli all got the nod.
Meanwhile, Juan Carlos Garrido, with a plethora of injury worries including Marcos Senna, Cani and most notably Italy striker Giuseppe Rossi, brought in Mateo Musacchio, Hernan Perez and Joselu into the team.
Villarreal began the game by defending deep, and their best opportunity of the half came when Jonathan De Guzman delivered a perfect long-range pass to Joselu but the striker’s poor touch saw the ball escape from his grasp as Joe Hart collected in his area.
Just before the half hour mark, Yaya Toure put Mancini’s men 1-0 up after an uninspiring opening spell. David Silva, alert and energetic, intercepted a pass by Gonzalo and the Spaniard charged forward, creating an opportunity for Toure who finished calmly, side footing Diego Lopez.
The goal, Toure's first since their infamous FA Cup triumph last season, changed the dynamics of the game: City began to dictate the play and the home fans at the El Madrigal became quiet.
Then, with the first half drawing to a close, Silva spotted Balotelli just outside the box and, as the striker drove powerfully forward, he was fouled by Musacchio and a penalty was awarded.
There was only one man who was going to take the spot-kick. Balotelli stepped up and coolly dispatched the ball into the bottom corner -sending the Diego Lopez the wrong way.
Silva was replaced by Adam Johnson on the 65th minute as the Spanish maestro went off clutching his hip, but by this point Villarreal looked a demoralised team and their problems were further exacerbated as City grabbed their third goal of the game.
Mancini’s team charged forward to find the home defence half asleep. Balotelli threaded a square pass to Toure and the Ivorian, with great composure, passed the last defender and slotted the ball into the net.
Sergio Aguero came on late in the game but it proved more of a run around for the Argentine striker as City coasted until the final minute of the match. Their triumph sets up a mouth-watering meeting with Napoli, and Mancini will know what victory will secure qualification to the knockout stages.