A brace from Jay Simpson and a beauty from Carlos Vela was enough to secure a spot in the next round.
Apart from the absence of the injured Emile Heskey, Wigan otherwise put out their strongest side. Arsene Wenger, despite the challenge posed by Steve Bruce's men, kept faith with his youngsters and arguably played a weaker team than that which demolished Sheffield United in the previous round.
Arsenal should have scored twice in the 14th minute. The first opportunity came when Fran Merida Perez slipped Vela in. The Mexican striker then outpaced Wilson Palacios, but Chris Kirkland got an outstretched hand to the ball as Vela tried to round him.
Vela regained possession and the ball eventually found its way to the right side with Jack Wilshere. The 16-year-old then threaded a ball for Simpson to run on to before firing a shot past Kirkland but onto the bar.
Kieran Gibbs had a good shot saved three minutes later, but the Wigan keeper had to be at his best on 20 minutes to parry an Aaron Ramsey free-kick that was destined for the top right-hand corner.
Vela came close again on 24 minutes when on the edge of the right side of the area he curled in a left-foot shot that was winging its way towards the top left corner, before Kirkland got an outstretched hand to turn the ball around the post.
Jason Koumas tested captain for the night Lukasz Fabianski on 26 minutes with a 20-yard drive that the Gunners keeper got the slightest of touches to to push the ball over the bar.
Wigan began to carve out more opportunities for themselves and Daniel De Ridder got himself in a good position but his shot from the right side was straight at Fabianski.
Arsenal took the lead on 42 minutes after a sublime pass from Wilshire. The youngster picked out a wondrous ball that carved open Wigan allowing Simpson to outstrip Mario Melchiot to toepoke the ball into the net from eight yards out.
Gibbs forced a good save out of Kirkland in the 62nd minute after the left-back accelerated on to a Ramsey through-ball and his powerful left-foot shot was blocked by the England keeper.
Simpson and Arsenal doubled their tally on 66 minutes after a swift counter-attacking move, the architects of which were Ramsey and Vela. The Welsh midfielder lifted a ball over the struggling Melchiot for Vela to sprint past Emmerson Boyce.
With just Kirkland to beat, the striker unselfishly squared the ball for Simpson, who fired a powerful shot into the net from inside the area.
The Mexican got his reward five minutes later when put through by Johan Djourou and under pressure from Titus Bramble he showed strength, composure, intelligence and disguise to spot Kirkland off his line to lob the ball into the net.
A wondrous double save from Fabianski with just three minutes left on the clock stopped Wigan from gaining a consolation goal. The first was a block from a De Ridder shot after the Dutchman jinked his way past a series of Arsenal players.
Then, the Polish kepper was up like a shot to throw himself in front of Amr Zaki to push his shot on to the bar and ensure his side's place in the last eight.