Gary Madine scored the only goal of the match from the penalty spot after 50 minutes as the Owls claimed the scalp of their Barclays Premier League opponents.
League Two Burton produced arguably the performance of the night as they thumped npower Championship outfit Leicester 4-2.
Goals from Chris Palmer (20), Cleveland Taylor (53), Robbie Weir (64 pen) and Jacques Maghoma (68) saw the visitors to a surprise victory.
Nick Ajose struck a last-minute winner as League One Crawley upset Bolton 2-1.
Benik Afobe fired Bolton ahead in the 21st minute and the Championship side looked on course for the win but Cork-born Billy Clarke levelled for the hosts in the 81st minute and Ajose popped up late on to send the Trotters out.
Blackburn boss Steve Kean suffered another setback in his bid to win over his doubters as Rovers crashed out after a 2-1 defeat at League One MK Dons.
Ireland’s James McClean scored in each half to lift Sunderland to a 2-0 win over Morecambe, while two shane Long goals helped West Brom past Yeovil, 4-2.
A Simon Lappin goal and Wesley Hoolahan’s penalty guided Norwich to a 2-1 win over Scunthorpe, while former Republic of Ireland midfielder Kevin Kilbane made two goals and scored the other in Coventry’s extra-time win over midlands rivals Birmingham.
James Collins bagged a hat-trick as Championship side Swindon got the better of Premier League Stoke 4-3 after extra-time, after Jon Walters’ 83rd-minute strike had made it 2-2 and seemingly given the home side the edge.
Goal of the night arguably went to Simon Cox of Nottingham Forest but the Ireland striker’s 25-yard drive could not stop his side crashing 4-1 at home to Wigan.