The Citizens made it 16 consecutive victories in all competitions to move 10 points clear at the top of the Premier League.
Phil Foden put the visitors ahead with a deflected shot on 32 minutes but Richarlison articulated a response for Carlo Ancelotti’s men from close range seven minutes before the interval.
Riyad Mahrez restored City’s lead midway through the second half with a sumptuous goal before Bernardo Silva settled Everton’s defeat on the 77th minute mark.
“A real tough game, pitch in not perfect condition in winter and they are so physical team. A solid performance, the guys ran like way we have to fight for the three points,” the former Barcelona and Bayern Munich coach said after the game.
"We have the quality up front but it comes through the passes and when we arrive in the final third we want to attack too quick, we have to have patient. The second goal is a an example of that, if you can't find (the opening), make an extra pass.
"Sometimes Riyad Mahrez plays left, sometimes right, it depends on the decisions for the team.
"Football is not about defensive, offensive, you cannot win titles (without a good defence) and we have concede few goals and few chances.
“This team (Everton) scored three at Old Trafford and five against Spurs and a team that can create chances.
"Sometimes our full-backs attack wider, it depends on the opponents. Not all the full-backs can play inside, it depends on the skills of everyone.