The scores remained tied at 0-0 until Ryan Williams converted a free kick in the 84th minute to grant his side passage into the next round.
Over at Boundary Park, Derby County ensured their progression into the next round following a 1-0 victory over Oldham Athletic – Michael Jacobs providing the vital goal midway through the first half.
Tranmere Rovers got off the a blistering start thanks to Andy Robinson, who found the net in just the second minute of the game. Chris Atkinson put Ronnie Moore's men 2-0 ahead in first-half injury time.
Coventry City midfielder Carl Baker turned from hero to villain against Leyton Orient as the Sky Blues battled bravely at the Matchroom Stadium. Baker broke the deadlock for the Sky Blues, but Kevin Lisbie and Dean Cox put the home side ahead before the break. Baker received his marching orders for a late challenge on Roman Vincelot in the 56th minute, but just moments later Franck Moussa drew his side level. However, Lisbie grabbed his second of the game to send the Orient through.
After an early own goal from Ben Nugent, Brentford recovered well in the second half, scoring twice in two minutes to take the lead. First, Farid El Alagui equalised, before substitute Martin Fillo gave the hosts the lead in the 64th minute. El Alagui then got his second in the 90th minute to take Brentford into the second round following Josh Scott's late equaliser.
A late goal from Andy Williams was enough for Swindon Town to reach the second round at the expense of Torquay United, while a Chris Hussey double, including a 90th-minute winner, saw Burton Albion win at Sheffield United after Michael Doyle's second-half equaliser.
Lee Tomlin scored a brace as Peterborough United dominated the second half in their 5-1 win over Colchester United. Joba Ibehre scored an equaliser for the home side in the 47th minute after Gabriel Zakuani gave the Posh the lead and from then on it was all the visitors as Tomlin, Tommy Rowe and Tyrone Barnet found the net.
Bury earned their place in the next round with a 3-2 win over Crewe Alexandra as Shaun Begley, Shaun Harrad and Richard Hinds scored the goals to send them through at Gigg Lane. Ben Reeves and Scott Banton found the net either side of half time to hand MK Dons victory over Northampton Town, while Craig Westcarr and James Baxendale sent Walsall through with a 2-1 away win over Port Vale.
Morcambe 1-0 Wolves, Tranmere 2-0 Mansfield, Leyton Orient 3-2 Coventry, Brentford 3-2 Dag & Red, Swindon 1-0 Torquay, Colchester 1-5 Peterborough, Bury 3-2 Crewe