A goal from teenager Jordan Ball on his senior debut was enough to give Doncaster Rovers a 1-0 win to knock Johnstone's Paint Trophy holders Chesterfield out of the competition.
Ball's first act after being introduced as a substitute after 83 minutes was to head home David Cotterill's deep corner and book his side's place in the next round.
Coventry City progressed through after a 4-0 second-half rout at York City.
Goals from David McGoldrick and Callum Ball, an own-goal from Jamal Fyfield and a further strike from Chris Hussey wrapped up the win.
Preston North End substitute Akpo Sodje scored twice to earn his side victory a 4-2 win at Morecambe.
Crewe Alexandra eased through to the third round after a slick display secured a 2-1 win at Shrewsbury Town. Luke Murphy and Max Clayton put the Alex 2-0 up before substitute Asa Hall pulled one back.
Bury went through after a a 5-4 penalty shoot-out win at Spotland against arch-rivals Rochdale.
Bradford City reached the third round 3-2 on penalties after a goalless draw at Hartlepool United.
Port Vale won a dramatic penalty shoot-out 6-5 to knock Walsall out after the two teams drew 2-2 in normal time at the Banks's Stadium.
Henoc Mukendi booked Northampton Town's place in the next round after they came from behind to beat 10-man Colchester United 2-1.
Northampton's early chance fell to Adebayo Akinfenwa who saw his header hit the bar before Freddie Sears broke the deadlock after half an hour, superbly volleying home a right wing cross from ex-Cobbler Ian Henderson.
But Akinfenwa equalised six minutes into the second half from the penalty spot after Kemar Roofe was upended in the box.
And three minutes later Henoc Mukendi opened his account when he converted a cross from the impressive Ishmel Demontagnac.
Super-sub Sam Saunders came off the bench to earn Brentford their second win in four days over Crawley Town as he scored the only goal in a 1-0 win.
Argentine midfielder Andres Gurrieri scored a superb 30th-minute winner as Plymouth Argyle beat Aldershot Town 2-1 after Paris Cowan-Hall and Craig Reid had earlier traded goals.
Moses Odubajo's first-half strike proved enough to hand Leyton Orient a 1-0 victory over winless Barnet.
Goals from Ryan Cresswell and Britt Assombalonga handed Southend United a 2-0 win over Dagenham and Redbridge at Roots Hall.
Oxford United twice hit back from behind to progress with a 4-2 win at Cheltenham Town.
Wycombe Wanderers' Dean Morgan bagged a brace to send npower League 1 opponents Portsmouth crashing out with a 3-1 victory at Fratton Park.