Carlisle had taken an early lead at the League Two side Rochdale, with Michael Bridges scoring after just four minutes.
But little over 10 minutes later they were behind after Lee Thorpe and Chris Dagnall scored for Dale.
Although Gary Madine levelled for the Cumbrians, they were beaten 4-3 in the penalty shootout.
Huddersfield fell at Darlington, with the defender Alan White scoring the only goal of the game.
Morecambe went through after a penalty shootout win over Chester at the Deva Stadium, the game had finished 1-1.
Andy Bishop's goal after 77 minutes gave Alan Knill's Bury a 1-0 win over Stockport County at Gigg Lane.
Shrewsbury Town claimed the result of the night in the southern section, recording a stunning 7-0 win at Wycombe Wanderers.
The forward Grant Holt scored five of the goals, including three in a five minute spell towards the end of the game.
Brighton and Hove Albion sent Orient packing, though only after a penalty shootout at the Withdean Stadium.
The tie had finished 2-2, with the Seagulls prevailing 5-4 in the shootout.
Colchester United were 1-0 victors at Gillingham, with the midfielder Mark Yeates scoring the only goal.
Mark Nwokeji's strike gave Dagenham and Redbridge an impressive 1-0 win at Peterborough United.
Bournemouth also claimed a League One scalp, with Darren Anderton's late goal giving them a 1-0 success at MK Dons.
Luton Town progressed at the expense of Brentford, winning a penalty shootout 4-3 after the tie at Kenliworth Road had finished 2-2.
Swindon Town beat Hereford United 2-1 at Edgar Street, and Walsall saw off Cheltenham Town at Whaddon Road by the same scoreline.