Liverpool edged out Leeds 1-0, Arsenal prevailed 2-0 against West Brom, Sunderland beat Birmingham by the same scoreline and Bolton overcame West Ham after extra time.
Stoke saw off Blackpool in a seven-goal thriller, Blackburn won 1-0 at Nottingham Forest and Portsmouth saw off Carlisle.
Burnley provided the main story of last season's competition with a giant-killing run to the semi-finals but the roles were reversed for their clash against Championship strugglers Barnsley as they started the night firm favourites to progress to round four but ultimately came unstuck.
The Clarets, who lost Brian Jensen and Martin Paterson to injury, took the lead through Steven Fletcher but they were trailing 2-1 by half-time after goals from Jon Macken and Anderson De Silva.
Chris Eagles drew Burnley level at 2-2 in the 52nd minute but Barnsley were not to be denied and Hugo Colace popped up with the winner 15 minutes from time.
Jermaine Beckford had a goal controversially disallowed for offside early on as Leeds made a bright start at Elland Road against a Liverpool side showing nine changes from the weekend clash with West Ham.
Beckford then missed a couple of good chances in the second half before David Ngog's neat finish in the 66th minute silenced the home crowd and Liverpool held on for a hard-fought victory.
Arsene Wenger trumped Rafa Benitez by changing his entire starting XI and Arsenal's youngsters, who so often earn rave reviews for their Carling Cup performances, saw off Championship leaders West Brom at Emirates Stadium.
The Gunners' class of 2009/10 were made to work hard for their success despite West Brom being reduced to ten men when Jerome Thomas was sent off in the first half.
The highly-rated Sanchez Watt scored the crucial opening goal on 68 minutes and Carlos Vela struck again moments later as Arsenal moved into the next round.
Stoke have turned the Britannia Stadium into a formidable fortress in the Premier League but they had to dig deep after Blackpool had produced a superb first-half performance to open up a 2-0 lead.
David Vaughan and Billy Clarke found the target either side of half-time to put the Seasiders in control before Liam Lawrence missed a glorious chance to reduce Stoke's arrears as Matthew Gilks kept out his penalty.
The Potters stormed back with a three-goal blitz in the space of five minutes thanks to Danny Higginbotham, Matthew Etherington and Ricardo Fuller but there was more drama still to come.
Ben Burgess scored to draw Blackpool level at 3-3 but Stoke responded again through Andy Griffin to seal a remarkable 4-3 victory.
Portsmouth made the long journey to Brunton Park desperate to avoid more disappointment following their torrid start to the Premier League season but they had to come from behind to beat League One outfit Carlisle 3-1.
Ian Harte fired the Cumbrians ahead from the penalty spot on three minutes before Aruna Dindane, Danny Webber and Anthony Vanden Borre scored their first goals for Pompey to turn the game around.
Sunderland came out on top against Birmingham in an all-Premier League affair at the Stadium of Light, with the damage done by early goals from Jordan Henderson and Fraizer Campbell.
West Ham bowed out of the competition following a 3-1 extra time defeat to Bolton at the Reebok Stadium.
Herita Ilunga opened the scoring for The Hammers on 59 minutes but Kevin Davies levelled with just four minutes of normal time remaining.
Gary Cahill then gave the Trotters an advantage early in extra time and Johan Elmander stuck again in the 119th minute to clinch victory.
Benni McCarthy's 37th minute free-kick proved decisive for Blackburn at the City Ground as Nottingham Forest slipped to a 1-0 defeat.
Forest earned a penalty in the second half but Dexter Blackstock was unable to beat Jason Brown as Rovers held on.
In the only all-Championship tie of the night, Peterborough proved too strong for Newcastle with a 2-0 victory at London Road.
Craig Mackail-Smith opened the scoring for Posh after 20 minutes and Tom Williams doubled their advantage 11 minutes later, while Danny Guthrie was sent off for the Magpies.
League Two side Port Vale, the lowest ranked team left in the competition, were knocked out by Scunthorpe after extra time at Glanford Park.
The scoreline was goalless after 90 minutes but Scunthorpe improved in extra time and ran out 2-0 winners courtesy of goals from Paul Hayes and Grant McCann.