Teams from the J1 League will take part in the tournament.
Sanfrecce Hiroshima, Gamba Osaka, Urawa Red Diamonds and FC Tokyo were given a bye to the quarter-finals due to qualification in the 2016 AFC Champions League.
The group winners and the runners-up of each group qualified for the quarter-final along with the four teams which qualified for the AFC Champions League.
FC Tokyo won 3-1 on aggregate.
Updated to games played on 15 October 2016Names of players in bold are still active.