Mario Balotelli did not do much in this game except score the opening goal, his first in the Premier League this season, yet it was enough to tilt the result Manchester City's way after Wigan Athletic had spent an hour looking more than capable of holding the defending champions to another scoreless draw.

Wigan even had chances to take the lead themselves before Balotelli pounced with a slightly scruffy goal to re-energise a tired-looking City. Many a manager would have hauled the under-performing striker off in favour of Carlos Tevez or Edin Dzeko before the 69th minute, but Roberto Mancini's patience paid dividends and once again one of his substitutes, James Milner, made victory safe with a stylish goal before departing with a pulled hamstring.

While sending Milner on for the disappointing Javi García was a routine substitution and an effective one, Mancini perplexed many observers by replacing Sergio Agüero with the defender Aleksandar Kolarov when the game was still goalless. "We still had enough offensive players," he explained. "We have four top strikers at the club and Mario is one of them, and I am happy he scored his first goal."

Internazionale have just denied they are interested in re-signing Balotelli, and on this evidence Nerazzurri fans would not consider they are missing out on much, although he did work harder than Agüero in the second half. Making a rare start for the visitors in the centre of the attacking three, Balotelli was a spectator in the first period, occasionally moving out to the left wing to try and see more of the ball.

Agüero was taking a turn in the middle when a mistake by Maynor Figueroa almost proved costly, Adrián López coming to the rescue after the Wigan defender's attempted clearance went straight to the City striker. Agüero had a clear run to goal from 40 yards out but could not quite summon the pace to shake off the rapidly arriving cover.

Thus reprieved, Wigan came back strongly, with Ronnie Stam twice showing Pablo Zabaleta a clean pair of heels down the right and Arouna Koné heading narrowly over from the second of his crosses. Jordi Gómez shaved an upright from a free-kick following a foul by Agüero, who found himself exposed in a defensive area through García's surprising reluctance to make a challenge.

City survived a penalty appeal right at the end of the first half when Gómez flung himself theatrically to the ground after the tiniest of shirt-tugs from Zabaleta, then the Wigan player earned a caution for taking out his frustration with a snap at Gareth Barry's ankles.

On the day when David Platt earned a two-match European ban for being sent to the stands against Real Madrid, and City themselves picked up a £10,000 fine for having five players booked in the same Champions League game, Mancini's side made it to the interval unscathed but saw Barry booked later for a retaliatory foul on Gómez.

Balotelli received his first clear goalscoring opportunity at the start of the second half – and missed. Maicon's cross from the right found the Italian unmarked at the far post and, though the angle was tight, Balotelli should have at least hit the target with a close-range free header.

Minutes later at the other end Koné was guilty of an even more glaring miss when James McCarthy's diagonal cross picked him out in front of goal, yet from a position near the penalty spot he sent his header yards wide. When neither Koné nor Gómez could get on the end of Jean Beausejour's useful cross after an hour Wigan must have begun to fear the worst.

Surprisingly Tevez and Dzeko remained on the bench even when Agüero was withdrawn, though as Balotelli struck within seconds it hardly seemed to matter. Milner and David Silva were involved in the buildup, before Ali al-Habsi spilled Barry's low shot to allow Balotelli to pick up the rebound and score at the second attempt. As goalkeeping errors go it was not up there with his howler against Reading, yet this time there was to be no redemption.

Milner beat him again three minutes later, the England midfielder meeting Silva's pass with a rising, curving drive from the edge of the area. In the space of a couple of attacks City had bagged the points.

"For 60 minutes we were the strongest side," Roberto Martínez said, not completely fancifully. "We were better on the ball than City but we couldn't find a way to score the first goal."