The Toffees were able to keep City out for the first hour of the match, before two goals in the final 30 minutes from substitutes Mario Balotelli and James Milner sealed all three points for the home side.
"We've never had an easy game against Everton," the Belgian told Sky Sports News. "I thought today especially we showed a lot of positives. Defensively we looked good.
"I'm really happy with the performance. With the quality we have, sometimes it's just a matter of patience and the goals will come."
Manchester City travel to Germany in midweek to take on Bayern Munich in the Champions League, before returning to Premier League action on Saturday at Ewood Park to face Blackburn Rovers.