Marcell Washington put the Young Gunners ahead with a powerful strike after neat build-up play, but Troy Perrett levelled for the hosts within two minutes. The match turned after Arsenal goalkeeper Alexei Rojas was sent off for a foul, and Cardiff took full advantage of the numerical edge with goals from Will Spiers and Trey George to secure progression to the knockout phase.
At Chesterfield, Liverpool Under-21s -- managed by former Wales boss Rob Page -- recovered from 2-0 down to draw 2-2 and then prevailed in a colossal penalty shootout, winning 11-10. Bailey Hobson had opened the scoring for the home side when his effort bounced past visiting keeper Fabian Mrozek, and Dylan Duffy doubled the advantage shortly afterwards. Kaide Gordon salvaged a point for Liverpool with two goals, the second coming in stoppage time. The shootout finished when John Fleck struck the bar with Chesterfield's 12th penalty, his second attempt in the sequence.
Even with the bonus point from the late equaliser and shootout, Page's side ended bottom of their group while Chesterfield advanced as one of the group's top two teams.
Swindon Town finished top of their group after the emphatic win at MK Dons, with West Ham United U21s second -- the only Premier League academy side to reach the knockout rounds this week.
The draw for the EFL Trophy last-32 is due to take place at 14:30 GMT on Thursday, 13 November.