The 3-0 defeat means Steve Bould's side have crashed out of the EFL Trophy.
It was a shocking night for the Gunners as William Saliba and Tim Akinola were both sent off with just minutes remaining.
Ryan Longman, Paul Osew and Joe Pigott scored from Wimbledon.
Veteran defender Sokratis also featured in the game, having been frozen out of Mikel Arteta's first-team squad.
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