[1][2][3] The cup winner was won a spot in the 2013–14 UEFA Europa League group stage.
CSKA and Zenit will be home teams in their pairs due to playing more away games than Yenisey and Kuban respectively in earlier rounds.
Yenisey from the National Championship is the lowest ranked team left in the competition.
The home teams in Zenit, Anzhi, Rostov and CSKA pairs were determined in a draw held on 18 April 2012.
Zenit and Rostov will be home teams in their pairs due to playing more away games than Yenisey and Kuban respectively in earlier rounds.