Edin Dzeko and substitutes Yaya Toure and Jesus Navas were also on target as City completed a routine 5-0 win over the Championship side at the Etihad Stadium.
City had made 10 changes from the team who thrashed Manchester United in Sunday's derby at the same venue but there was no let-up in the intensity of their performance.
From the outset there was never any danger of Wigan repeating their heroic FA Cup final success over City from May. Dzeko opened the scoring with a fine volley 12 minutes before the interval and Jovetic, who had hitherto endured a frustrating night, bundled in the second on the hour.
Toure came off the bench to curl in what is now becoming a trademark free-kick from 20 yards - his third such effort of the season - before £24m signing Jovetic netted a second from close range. Navas rounded off the scoring four minutes from time when he broke through to shoot low past Lee Nicholls.
City's style of play and clinical execution were just as manager Manuel Pellegrini had desired, and provided evidence that the fluid system he is introducing throughout the club is taking hold. Of his starting line-up, only midfielder Fernandinho survived from the side which began the 4-1 defeat of United.
Micah Richards came in for his first appearance of the season and impressed after recovering from injury while James Milner looked dangerous on the left and youngster Marcos Lopes had a fine full debut.