Mario Balotelli, making his first appearance in the competition this season, was also on target from the penalty spot as City recorded back-to-back wins over the Spaniards to move second in Group A.
It was a result that rarely seemed in doubt as City dominated at El Madrigal but of possible concern to them was the sight of the influential David Silva leaving the field clutching his back.
Otherwise Mancini's only headache may have been the physical one he received when jumping up and banging himself on the roof of the dugout during the first half.
Aside from a nervy opening couple of minutes, City controlled the game throughout and, after patiently awaiting their first goal on 30 minutes, never looked like yielding.
Their hopes of reaching the knockout stage could still hinge on their next vital away assignment at Napoli but they at least now have a two-point advantage over the Italians and a win will make certain.
Until tonight, City's imperious domestic form had not been matched in Europe and they were again uncertain at the start.
Villarreal were determined to give the visitors as little time in possession as possible and pressed City into an early mistake.
Jonathan de Guzman seized the ball in midfield and fed Hernan Perez but his long-range shot was easily claimed by Joe Hart.
It was a positive start by the injury-ravaged Spaniards, whose form in their own domestic competition has been poor.
City did manage to get hold of possession for good spells but it soon became apparent they would have to be patient against the resilient hosts.
It was not until the 20th minute they seriously threatened when Samir Nasri fired wide.
The home supporters were incensed as City were allowed to build an attack while a Villarreal player was off the field and they whistled even louder as Silva won a free-kick outside the box.
After some arguments and bookings for Wakaso Mubarak and Balotelli, Silva stepped up to take the set-piece and curled into the wall.
Yet Silva, a former hero at nearby Valencia, remained the dangerman and stole possession from the feet of Perez to set up the opening goal for Toure on the half-hour.
The dynamic Ivorian raced through as Silva slid a perfect pass into the box and opened his body to sidefoot past Diego Lopez with cool precision.
Villarreal tried to respond but De Guzman horribly sliced a shot into the crowd from a promising position.
Nasri had a similar opportunity at the other end but failed to make a clean connection and Lopez was not troubled.
De Guzman hit another shot with greater accuracy but it was straight at Hart.
City doubled their lead from the penalty spot in time added on at the end of the first half after Mateo Musacchio clipped the ankles of Balotelli.
Villarreal protested but Balotelli held his nerve - despite apparent attempts from someone in the crowd to put him off with a laser pen - and firmly dispatched a low shot after stuttering in his run-up.
Mancini returned for the second half with an ice pack on his head but his team were not in any discomfort.
City carried their dominance into the second half, Silva wining another free-kick in dangerous territory after a menacing run but Balotelli's shot was deflected wide.
Nasri then found more space but skewed a low shot wide.
Villarreal seemed broken and had little to offer aside from a tame shot from former West Brom midfielder Borja Valero that Hart claimed easily.
Silva, who had caused the hosts numerous problems, was withdrawn by Mancini midway through the second half, possibly because of injury, to a generous ovation from all sides of the ground.
City carried on without him, Toure claiming his second after 71 minutes with a goal that made the game look all too easy.
Nasri fed Balotelli down the left and the striker looked up to pass inside for Toure, who casually glided past Jose Catala before stroking the ball past Lopez.
It proved Toure's last involvement with Mancini replacing him with Aguero moments later.
Aguero, accused of mocking Villarreal players after his late winner against them a fortnight ago, found himself jeered as he ran on.
The game was long won for City and it almost became a training exercise as they wound down the closing minutes and the ground emptied.