‘Wish me luck, this will be life-changing for all the three qualifiers – whoever they are’
Everton had won seven of the previous eight matches between the two teams, including four consecutive victories in Manchester.
But Balotelli provided Roberto Mancini with a first victory over the Goodison Park club with a goal mid-way through the second half before Milner added a second late on.
The victory saw City go one point clear of rivals Manchester United at the top of the table, although United need only a point from their game at Stoke later on Saturday to reclaim top spot.
City now head to Bayern Munich on Tuesday with five wins from their six Premier League matches this season.
Everton started brightly, with Jack Rodwell shooting narrowly wide from the edge of the area and Leighton Baines also going close after cutting in from the left flank.
City struggled to penetrate in the final third and only had a Sergio Aguero pass that just evaded David Silva to show for their early pressing.
They also threatened when Edin Dzeko surged through on to Phil Jagielka’s poor header but the Bosnian’s touch past Tim Howard took him too wide.
Samir Nasri also drove wide from just outside the area as City looked to shake off their early anxiety, while Aguero shot wide after being picked out by Yaya Toure’s low pass.
Everton’s task was made considerably harder when Rodwell, Phil Neville and Leon Osman were all cautioned in the space of a few minutes.
But City’s frustration continued when Dzeko hooked a shot well off target from a neat Micah Richards cross from the right.
Howard also pulled off a fine save, pushing away Aguero’s curling shot, with Dzeko unable to get a touch.
And Gareth Barry’s 25-yard drive was held by Howard as Everton, with just midfielder Tim Cahill playing on his own in attack, struggled to get out of their own half.
Sylvain Distin was forced to turn a Silva cross past the post as the pressure continued after half-time, with Aguero lifting yet another shot over the bar from just outside the area.
Leon Osman had an effort held by Joe Hart as Everton enjoyed a rare break forward.
Another quick break from Everton saw Seamus Coleman break into the City half before hitting a deep cross that Cahill headed just past the top corner.
City manager Roberto Mancini hinted at his increasing frustration when he replaced Dzeko with Balotelli with an hour gone.
Everton then suffered a blow when Cahill, who came off second best in a challenge with Vincent Kompany, had to be replaced by Louis Saha with what looked to be an ankle injury.
And Howard had to beat away a stinging shot from Nasri as Everton waited to make that change.
But midway through the second half, City finally made their breakthrough when Aguero cut in from the right and flicked the ball to Balotelli, who found the bottom corner of the net from 20 yards via a deflection.
City came close to adding a second when Balotelli picked out Silva and the Spaniard’s low shot came back off the post.
The hosts added a second when Silva clipped a sublime pass through and Milner guided a shot past Howard.
‘Wish me luck, this will be life-changing for all the three qualifiers – whoever they are’
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