Scott Wagstaff scored a late winner as Charlton came from behind to beat MK Dons 2-1 and reach the third round of the Johnstone's Paint Trophy.
Second-half goals from Pawel Abbott and Wagstaff cancelled out Luke Chadwick's early opener and handed the Addicks their second victory over the Dons in eight days.
Brentford beat Leyton Orient 5-4 on penalties after the sides had finished goalless after 90 minutes.
Goalkeeper Richard Lee was the Bees hero, diving to his right to save a Matthew Spring spot-kick after both sides had successfully converted their first four kicks.
David Ball scored his first goal for the club as Swindon overcame Torquay 2-0 to ensure a comfortable passage into the last 16.
Exeter coasted through to the third round after beating struggling Hereford 3-0 with goals from Daniel Nardiello, John O'Flynn and Richard Duffy.
Matt Paterson netted twice as 10-man Southend cruised into the quarter-finals after with a 3-1 victory in an ill-tempered game with Barnet.
Will Hoskins volleyed a 90th-minute winner to knock battling Aldershot out courtesy of a 1-0 win.
Plymouth eased into the quarter-finals as Steven MacLean and Craig Noone struck either side of half time to secure a 2-0 win over Cheltenham.
Wycombe scored two late goals through Kevin Betsy and Scott Davies to claim a 2-0 victory over Colchester.
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