The Capital club had looked the better side for large parts of the game at Station Park, taking the lead through Ouzy See on six minutes and regaining the advantage through a wonderful Lee Hamilton bicycle kick after Jordan Allan had equalised for the hosts.
Hibs loanee Josh Campbell smacked a fierce volley off the post that, had it gone in, would have put City 3-1 up but Roberto Nditi’s 94th-minute strike forced extra time and despite the hosts losing Hamish Thomson to a straight red City were unable to capitalise, with penalties needed to decide the tie.
Liam Henderson, Liam Brown, and Marc Laird all converted from the spot but when Daniel Hoban saved substitute Craig Thomson’s penalty, Daniel Scally stepped up to fire the League One side into the fourth round.