Neil Harris' Lions will visit Roots Hall in the next round of the competition.
Southend United have been drawn at home to Millwall in the area semi-final of the Johnstone's Paint Trophy.
The tie was pulled out live on Soccer AM, with the other area semi-final pairing League 2 sides Oxford United and Yeovil Town together.
A date and prices for tickets will be announced in due course.
Blues defeated Millwall at the Den earlier in the season 2-0, with goals coming from David Mooney and Adam Barrett.