Late goals by William Gallas and Tomas Rosicky moved Arsenal three points clear at the top of the Premier League.
Gallas celebrates scoring Arsenal's opener with help from Sagna
In the first half, a superb save from Mike Pollitt denied Emmanuel Adebayor and Emmanuel Eboue missed his kick when he looked certain to score.
Arsenal were relieved that Marcus Bent and Paul Scharner headed chances wide.
Wigan looked set to snatch a draw, but Gallas headed in on 83 minutes and Rosicky rounded off a breakaway move to seal the win two minutes later.
With Manchester United beaten at Bolton, the result gave Arsenal clear space at the top of the table.
But for a long time it looked as though a win would elude the Gunners.
Wigan put on a brave display and their doggedness would have pleased incoming boss Steve Bruce, who was watching from the stands.
Bruce would have particularly enjoyed Titus Bramble's decisive intervention to cut out an Adebayor cross set to be converted by Theo Walcott.
And the former Birmingham manager would also have noted Wigan's ability to break and create chances of their own - most notably headers from Bent and Scharner that were not far off target.
In fact, Bent had thought he had scored in only the fifth minute when he rounded keeper Manuel Almunia, but the offside flag denied him.
But for most of the first 45 minutes, Wigan - as expected - found themselves deep in their own half, repelling Arsenal attacks.
Their task was initially made easier by Arsenal's inability to find top gear, with the untried midfield pairing of Denilson and Lassana Diarra not a match for the unavailable Cesc Fabregas and Matthieu Flamini partnership.
And, at times, it appeared Rosicky had caught the English disease of squandering possession.
Ironically, Arsenal's only Englishman on show, Walcott, was slick with his passing, direct with his movement and by far the biggest threat on the pitch.
He set up the Gunners' best chance in the first half when he played an excellent one-two with Adebayor, whose shot was superbly saved by Mike Pollitt.
And the England teenager showed more sharp skills when he sped to the byline and cut the ball back to Eboue, only for the Ivorian to fail to get a boot on the ball.
After the break, Arsenal attempted to come forward with more purpose, but for all of the quick passing they were clearly lacking the invention of the suspended Fabregas and the guile of the injured Alex Hleb.
Their pressing almost led to a goal when Adebayor's strong running took him deep into the box but the striker dragged a shot across the face of goal and no-one was there to follow up.
At the other end, a mix-up between Kolo Toure and Gallas presented Bent with a chance but he screwed his shot wide.
Then Pollitt just about managed to bat away Denilson's free-kick at the near post and Wigan looked to set to take a point away from the Emirates Stadium.
But with seven minutes left, Bacary Sagna's cross to the near post was headed in by Gallas to put Arsenal ahead.
And then Rosicky made the game safe as Arsenal launched a rapid counter-attack, ending in the Czech international slotting home.
The one blow for Arsenal will be the injury to Walcott, who was stretchered off late in the game after a heavy tackle by Emile Heskey.
Arsenal boss Arsene Wenger:
"We needed something special and some patience to find an opening, and Gallas found it.
"He is a forgotten centre-forward because he knows where to be in the box and he can always turn up with a goal.
"Once again we found the resources to win the game. It is not the first time, so I do not feel it is a coincidence."
Wigan caretaker boss Frank Barlow:
"We play well for 80 minutes but we have to eradicate the problem we have of conceding goals in the last 10 minutes.
"The biggest disappointment for us is that we conceded a goal from a cross after we had fought off all their passing football.
"But the players showed great attitude and responded well to a brief chat from the new manager Steve Bruce before the game."
Arsenal: Almunia, Sagna, Toure, Gallas, Clichy, Eboue (Eduardo 68), Denilson, Diarra, Rosicky, Adebayor, Walcott (Bendtner 79).
Subs Not Used: Lehmann, Senderos, Song Billong.
Goals: Gallas 83, Rosicky 85.
Wigan: Pollitt, Boyce, Granqvist, Bramble, Kilbane, Brown, Scharner (Skoko 90), Landzaat, Olembe (Heskey 68), Koumas, Bent (Sibierski 84).
Subs Not Used: Kirkland, Hall.
Booked: Brown, Granqvist, Bent, Heskey.
Ref: Peter Walton (Northamptonshire).