In a tight Southern Group E, Colchester United beat Arsenal U21s 3-0 and Leyton Orient won 3-1 at MK Dons to advance.
Burton Albion’s thumping 5-2 win against already-qualified Northampton Town meant Notts County’s 1-0 home over Leicester City U21s wasn’t enough for the Magpies to sneak through to the knockouts, going out with an inferior goal difference despite accruing six points.
Crisis club Reading beat Newport County 3-0 to go through as runners-up behind Cheltenham Town in Southern Group H.
Elsewhere, Tranmere Rovers beat Stockport County 2-0 to join the Hatters in the knockouts, while Salford City resisted a late fightback to beat Wolverhampton Wanderers U21s 3-2.
Port Vale beat Wrexham 3-1 on penalties after the match ended 1-1 at Vale Park, with both sides going through.
Aston Villa became the only Premier League U21s outfit to reach the last 32 despite losing 3-0 at Barrow, while Blackpool beat Harrogate Town 5-4 on penalties after the game finished 2-2.
Walsall comfortably beat Shrewsbury Town 3-0 to advance as Charlton Athletic took maximum points from Southern Group C with a 1-0 victory over Bromley.
Gillingham finished bottom of Southern Group D despite their 5-4 penalty shootout win at Stevenage, who joined last year’s winners Peterborough United in the hat for the next round.
