The England international set up Noni Madueke for the opener on 11 minutes with a wonderful through ball and he repeated the trick eight minutes later when he sent Gabriel Martinelli clear to score his tenth goal in cup competitions this season for Mikel Arteta's side.
Bukayo Saka's cross was then turned in his own net by Jack Hunt before Gabriel Jesus beat the offside trap to race onto Christian Norgaard's ball over the top to lift a fine finish beyond Wigan keeper Sam Tickle on 27 minutes.
It looked at that point like Arsenal were going to run up a cricket score, but that proved to be the end of the scoring - with substitute Viktor Gyokeres hitting the post in the second half and Tickle saving well to deny Eze and Martinelli.
GOAL rates Arsenal's players from Emirates Stadium.
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