City gained some revenge for their FA Cup final defeat by the Latics in May as Edin Dzeko opened the scoring.
Jovetic scored twice, either side of Yaya Toure's free-kick, as City's class shone through in the second half.
Jesus Navas netted a late fifth as City eased into the fourth round.
Stevan Jovetic
Born: Titograd, 2 November 1989
Nickname: The Montenegrin Messi
Previous clubs: Mladost Podgorica, Partizan Belgrade, Fiorentina
International: Montenegro - 27 caps, 10 goals
City also hit the bar twice and forced Wigan's debutant goalkeeper Lee Nicholls into a number of excellent saves as they overwhelmed Owen Coyle's Championship side.
Their dominant display was even more impressive considering they made 10 changes to their team which hammered neighbours Manchester United on Sunday - Fernandinho the only player to retain his place.
Nicholls, who spent last season on loan at League Two side Northampton Town, tipped Dedryck Boyata's header over, while City's 17-year-old Portuguese midfielder Marcos Lopes hit the bar with a powerful shot.
The opening goal finally came when Dzeko calmly slotted home following Fernandinho's superb pass.
Wigan barely figured as an attacking force and Stephen Crainey almost turned spectacularly into his own net in the second half as the hosts continued to do most of the attacking.
They got their second when Jovetic bundled in at the second attempt before substitute Toure whipped a free-kick over the wall and into the back of the net.
Montenegrin striker Jovetic scored another from close range before Navas broke clear and rifled in the fifth from 10 yards out following Ryan Shotton's poor clearance.
Manchester City manager Manuel Pellegrini:
"I spoke with the players before we started the game, telling them we must always try to play the same way.
"We can change names but for me it was very important to see the same team we saw last Sunday, the same philosophy of football and the same high performance.
"I think it is very important for Stevan. He wasn't playing normally because he had some physical problems but the last two weeks he has been working hard and I am sure he is going to be a really important player for us."
Wigan manager Owen Coyle:
"We worked ever so hard, playing against one of the elite clubs of world football, let alone English football.
"They made 10 changes and their team was probably worth about £200m. There is no getting away from it, we knew it was a tough ask.
"As if their starting line up wasn't enough, I think the three subs they brought on probably added another £100m to the tally, but I am disappointed to lose by any margin of goals."
LINEUP, BOOKINGS (2) & SUBSTITUTIONS (6)
Manchester City
30 Pantilimon
02 Richards
06 Lescott
22 Clichy
38 Boyata
07 Milner
14 Garcia
25 Fernandinho (Toure - 46' )
64 Lopes (Navas - 71' )
10 Dzeko (Negredo - 79' )
35 Jovetic
Substitutes
29 Wright
13 Kolarov
33 Nastasic
08 Nasri
15 Navas
42 Toure
09 Negredo
Wigan Athletic
13 Nicholls
03 Crainey (Redmond - 68' )
06 Rogne
17 Boyce
25 Barnett Booked (Shotton - 59' )
07 McCann
14 Gomez
18 Espinoza
20 Fyvie Booked
23 Garcia
29 Dicko (Powell - 80' )
Substitutes
01 Carson
04 Shotton
43 Buxton
11 McClean
16 McArthur
19 Powell
28 Redmond
Ref: Friend
Att: 25,519
MATCH STATS
Possession
37%
63%
90mins
Manchester City
Wigan Athletic
Shots
243
On target
120
Corners
81
Fouls
1912
Live Text Commentary
90:00 +2:23 Full time
Full Time
The referee signals the end of the game. 90:00 +1:46 Clearance by Emmerson Boyce. 90:00 +0:47 Gael Clichy takes the free kick. 90:00 +0:21 The referee gives a free kick against Jordi Gomez for handball. 90:00 +0:18 Gael Clichy restarts play with the free kick. 90:00 +0:14 Free kick taken by Thomas Rogne. 89:42 Unfair challenge on Nick Powell by Yaya Toure results in a free kick. 89:34 Clearance by Thomas Rogne. 89:27 Clearance made by Thomas Rogne. 89:25 The ball is delivered by Gonzalez Jesus Navas. 88:24 Free kick taken by Fraser Fyvie. 87:47 Unfair challenge on Jordi Gomez by Gael Clichy results in a free kick. 86:59 Clearance by Ryan Shotton. 86:35 Jordi Gomez restarts play with the free kick. 86:29 Unfair challenge on Nick Powell by Yaya Toure results in a free kick. 85:20 Assist by Alvaro Negredo. 85:20 Goal scored
Goal! - Gonzalez Jesus Navas - Man City 5 - 0 Wigan
Gonzalez Jesus Navas grabs a goal with a right foot finish. Man City 5-0 Wigan. 83:58 Short corner worked by Gonzalez Jesus Navas. 83:45 Clearance by Thomas Rogne. 83:43 Centre by James Milner.
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