Yaya Toure’s first-half penalty consigned Everton to a defeat by the narrowest of margins at the Etihad Stadium.
The stand-in Manchester City skipper scored the only goal of the game from the spot after Phil Jagielka had been harshly adjudged to have bundled over James Milner in the area.
The Blues battled to the end and played with much more energy in the second half compared to the previous outing againsrt Hull - but crucially they could not find the necessary breakthrough.
Romelu Lukaku came closest to grabbing an equaliser, only to be denied by an athletic save from Joe Hart late on.
The game started with the hosts losing Sergio Aguero inside the opening five minutes; the Argentine striker limped off with a knee injury after receiving extensive treatment.
There was also a momentary fear that Samuel Eto’o – one of two changes to the Everton team from Hull – was close to seeing his involvement curtailed early too when he was rashly kicked in the lower back by Eliaquim Mangala when defending a corner. City’s £31million signing was lucky to get away with just a yellow.
And so was Fernando when he launched into an unbelievably high challenge on Gareth Barry, minutes after the home side had gone ahead midway through the first half.
Referee Andre Marriner had awarded what appeared to be a soft penalty against Jagielka on Milner – which was converted by Toure – when he then decided that Fernando’s boot to Barry’s head was only worthy of a booking.
The midfielder – making his first appearance for Everton against his former club – was left dazed from the incident, while Roberto Martinez left furious as he watched on from the technical area.
Decisions weren’t going the Blues’ way and they had to dig in to prevent Manchester City from extending their advantage in the lead up to the interval. Samir Nasri saw a fierce drive bravely blocked by Sylvain Distin, Jesus Navas dragged an effort wide from the edge of the box and Martin Demichelis headed over from a corner.
Kevin Mirallas was Everton’s brightest player in the first half and he went closest with a half-volley from 20 yards which was deflected around the post.
The immediate moments after the restart started with Everton soaking up pressure from Manchester City - substitute Jose Pozo was denied his first Premier League goal by a fine reaction save from Tim Howard.
Ross Barkley then came on for Muhamed Besic on 55 minutes and his introduction immediately saw the Toffees playing with more purpose and urgency.
The England midfielder set up Mirallas, who cut in from the left and had a goal-bound shot charge down by Mangala, before later teeing-up Eto’o whose drive was deflected just past the post.
The Cameroon striker should have done better when he was presented with another opportunity from a similar position, this time clipping the ball well over the bar.
Everton fought to the last whistle but they knew it wasn’t going to be their day when Hart produced a superb save from Lukaku in the closing stages.
Eto’o played an intelligent slide-rule pass to the striker but the England keeper was even to the powerful effort, diving full stretch to his left to produce a truly world-class save and ensure his team secured all the points.