However, the German scored again in between strikes from Theo Walcott and Aaron Ramsey to earn the hosts a victory which sees them climb above capital rivals Tottenham Hotspur into the final Champions League qualification spot.
Below, Sports Mole analyses whether the result was reflective of the action at the Emirates Stadium.
On target: 12
On target: 5
Was the result fair?
Arsenal were the better side, but the margin of defeat rubs salt into the Wigan wounds, because for large periods of the game they made this an even contest. The Gunners started and finished the match stronger and were good value for the points on the night.
Driven by Walcott and Santi Cazorla, the hosts began rapidly and were so dangerous going forward, particularly down the right flank, from where a couple of their goals were created. On the opposite wing, Kieran Gibbs excellently combated the trickery and pace of Callum McManaman as the Arsenal defence largely prevented Wigan from building momentum. Credit must also go to Wojciech Szczesny, who produced a wonderful save to keep his side level at a crucial point in the game.
Perhaps physically and mentally drained by their FA Cup triumph just 72 hours prior, Wigan started very slowly and were behind early on courtesy of their failure to defend a corner. Further mistakes from the centre-backs allowed Arsenal to establish a two-goal lead, and from there, even Roberto Martinez could not summon a miraculous comeback. Maloney had his moment of magic, but neither Arouna Kone, James McCarthy or Jordi Gomez were at their best on a night when it was crucial that Wigan took the chances that came their way.
Sports Mole's man of the match
Theo Walcott: Walcott was so direct with his running and gave Roger Espinoza a torrid time all evening, while his presence on the counter-attack meant that Wigan could not commit as many bodies forward as they would have liked. He again provided a winning contribution by scoring the vital second goal that set Arsenal en route to victory, and perhaps the Champions League.
Paul Scharner may be a Wigan favourite, but he was at fault for two of Arsenal's strikes this evening. He ducked the Gunners corner that was converted by Podolski and then fell asleep, allowing the German to lob Joel Robles for their third goal.
Arsenal may argue that Mike Dean's awarding of the free kick that led to Wigan's equaliser was soft, but it did not prove to be costly for the hosts. This was a fairly quiet night for the officials.
Arsenal: A trip to Newcastle United on Sunday, where victory would guarantee them Champions League football. Anything else could allow Spurs to snatch fourth spot.
Wigan: A Premier League finale against Aston Villa, which could also turn out to be Martinez's last game in charge at the DW Stadium.