The 14 winners from the first round and last year's cup finalists, Čelik and Rudar, compete in this round. Starting with this round, all rounds of the competition will be two-legged except for the final. The first legs were held on 3 October 2012, while the second legs were held on 24 October 2012.[3]
The eight winners from the second round competed in this round. The first legs took place on 7 and 21 November 2012 and the second legs took place on 21 and 28 November 2012.