In Southern Group F, **Leyton Orient** needed a big victory over **Barnet** to claim an unlikely second-placed finish on goal difference, but they were well beaten at The Hive, with Jack Maskell's first-half strike setting the hosts on the way to a 4-2 win.
**Oxford United** coasted to a 4-0 win over **Cheltenham Town** to pip the Robins to the runners-up spot in Southern Group A.
In Southern Group G, **Gillingham** made sure of their place in the last 16 by seeing off **Northampton Town** 2-1. The Gills only needed a point to be certain of finishing in second place above Brighton & Hove Albion U21, but Lamin Sillah scored one goal and made another to inspire his side to victory over their League Two rivals.
Elsewhere, a close-range shot by Tom Graves put **Crewe Alexandra** on track for the win they needed to progress from Northern Group B, but **Wigan Athletic** scored twice in the second half to dash their hopes, while veteran forward Nick Powell was among the scorers as **Bradford City** thumped **York City** 4-0 to top Northern Group C.
In a thriller in Northern Group D, already eliminated **Mansfield Town** looked set for their first points of the competition as they led already qualified **Chesterfield** 3-1 with 28 minutes remaining. But Dylan Duffy scored two of four goals in the closing stages to earn the Spireites a remarkable 5-3 victory.
Seb Campbell crashed home a 99th-minute winner as **Plymouth Argyle** beat **Swindon Town** at Home Park to finish top of the pile in Southern Group E, while there were also wins for **Huddersfield Town** - who thumped **Liverpool U21** 4-0 in Northern Group H - and **MK Dons**, who won 2-1 at Bromley to finish top of Southern Group H.
**Stockport County** beat **Tranmere Rovers** on penalties in Northern Group E, but both sides were already sure of qualification, while **Colchester United** beat **Ipswich Town U21** on penalties after a 0-0 draw in Southern Group D, in a match where both sides knew their campaign had ended after their second fixture.