Midfielder Michael parkins gave City the lead before Pat Dunning levelled for the visitors.
Two late goals from Stuart Fleetwood and sub Jon Kift eased City home.
The reward for the Bluebirds is a home tie against premiership Charlton Athletic in round 3. Date to be confirmed.
Captain Byron Anthony, who led the Bluebirds last night, has today been called into the Wales U19 suad for a mini tournament in Noerthern Ireland later this month.