Troubled Reading gained some respite, thrashing Arsenal Under-21s 5-2 to maintain their 100% winning record in the competition.
Kelvin Ehibhatiomhan scored twice for the Royals, who are bottom of League One, but missed out on a hat-trick when Ovie Ejeheri saved his penalty kick.
Arsenal's Fabio Vieira converted a spot-kick and had another saved, while Khayon Edwards hit his side's second.
Caylan Vickers, Harvey Knibbs and Sam Smith were also on target for Reading.
Aaron Pressley's double helped Stevenage - who were already unable to qualify - to finish their campaign in style, triumphing 5-2 against Crystal Palace Under-21.
Following an early own goal by Palace's Joe Sheridan, Jake Forster-Caskey and Harvey White also scored for Stevenage, who brought on 15-year-old goalkeeper Max Woodford late on to become their youngest ever debutant.
There was a similar landmark at Shrewsbury Town, where midfielder Simba Nyamwanza marked his 16th birthday by becoming their youngest first-teamer in a 3-2 victory at home to Walsall.
Also in the Southern section, Antony Evans netted the only goal for Bristol Rovers as they won at Newport County to go through at the expense of their hosts.
In the Northern section, holders Bolton Wanderers continued their perfect start in defence of the trophy, with Jon Dadi Bodvarsson's first-half double earning a third straight victory as they won 2-0 away to Stockport County.
Goalkeeper Ben Amos was the hero for Wigan Athletic, producing two saves in their penalty shoot-out victory following a 0-0 draw against Tranmere Rovers at Prenton Park.
Amos denied Sam Taylor and Dan Pike from the spot to secure a 6-5 success for the Latics, who progress as runners-up in their group.
Jake Beesley netted both goals for Blackpool as they ended with a 100 per cent record by winning 2-1 at home to Morecambe, with Farrend Rawson's late strike not enough to prevent the Shrimps' elimination.
A goal in each half by Jordan Gibson ensured Carlisle United finished on a winning note, overcoming Harrogate Town 2-0 at Brunton Park, although both sides go out in the group stage.