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 progressed through after a 4-0 second-half rout at York.
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 substitute Akpo Sodje scored twice to earn his side victory a 4-2 win at Morecambe.
Crewe eased through to the third round after a slick display secured a 2-1 win at Shrewsbury.
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 reached the third round 3-2 on penalties after a goalless draw at Hartlepool.
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's place in the next round after they came from behind to beat 10-man Colchester 2-1.
Northampton's best 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 Henderson.
But Akinfenwa equalised six minutes into the second half from the penalty spot after Roofe was upended in the box.
And three minutes later 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 as he scored the only goal in a 1-0 win.
Argentine midfielder Andres Gurrieri scored a superb 30th-minute winner as Plymouth beat Aldershot 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 & Redbridge at Roots Hall.
Oxford twice hit back from behind to progress with a 4-2 win at Cheltenham.
Wycombe's Dean Morgan bagged a brace to send League One opponents Portsmouth crashing out with a 3-1 victory at Fratton Park.
- Callum Ball
- David Cotterill