The winners and runners-up of each of the eight groups in the group stage qualified for the knockout stage. Both West Zone and East Zone had eight qualified teams.
In the knockout stage, the 16 teams played a single-elimination tournament, with the teams split between the two zones until the final. In the quarter-finals and semi-finals, each tie was played on a home-and-away two-legged basis, while in the round of 16 and final, each tie was played as a single match. The away goals rule, extra time and penalty shoot-out were used to decide the winner if necessary. Starting from this season, the knockout stage was split between the two zones until the final, similar to the AFC Champions League.
Schedule
The schedule of each round was as follows.
Bracket
The bracket of the knockout stage was determined as follows:
Round of 16:
Quarterfinals:
Semifinals:
Final: Winner SF1 vs. Winner SF2
Round of 16
In the round of 16, the winners of one group played the runners-up of another group from the same zone, with the group winners hosting the match. !colspan=3|West Zone !colspan=3|East Zone
West Zone
---- ---- ----
East Zone
---- ---- ----
Quarter-finals
In the quarter-finals, the four teams from the West Zone were drawn into two ties, and the four teams from the East Zone were drawn into the other two ties, with the order of legs also decided by the draw. The draw for the quarter-finals was held on 9 June 2016, 15:00 MYT, at the Petaling JayaHilton Hotel in Kuala Lumpur, Malaysia. There was no seeding or country protection, so teams from the same association could be drawn into the same tie. !colspan=5|West Zone !colspan=5|East Zone
West Zone
Al-Quwa Al-Jawiya won 5–1 on aggregate. ---- Al-Ahed won 3–0 on aggregate.
East Zone
Johor Darul Ta'zim won 3–2 on aggregate. ---- Bengaluru FC won 1–0 on aggregate.
Semi-finals
In the semi-finals, the two quarter-final winners from the West Zone played each other, and the two quarter-final winners from the East Zone played each other, with the order of legs determined by the quarter-final draw. !colspan=5|West Zone !colspan=5|East Zone
West Zone
Al-Quwa Al-Jawiya won 4–3 on aggregate.
East Zone
Bengaluru FC won 4–2 on aggregate.
Final
In the final, the two semi-final winners played each other, with the host team decided by a draw, held after the quarter-final draw.