Indonesia was formally notified over the weekend that it had been suspended by football's world governing body FIFA and the AFC confirmed on Wednesday the bans would include the World Cup and 2019 Asian Cup qualifiers.
Indonesia had been drawn in Group F for the next round of matches, which doubles as qualifiers for both tournaments, but has been excluded from the competition.
They were scheduled to play Taiwan on June 11 and Iraq five days later but the AFC said those matches had been cancelled.
Asia's regional governing body said the ban on Indonesian national and club teams would also extend to a range of other tournaments.
FIFA did allow Indonesia's national team to continue playing at the Southeast Asian Games in Singapore because the tournament has already started but all other penalties stand.
Indonesia was banned after the country's Sports and Youth Ministry cancelled of the domestic football season because of a row over which teams are eligible to compete in the Indonesian Super League (ISL).
The Indonesian Professional Sports Agency (BOPI), sanctioned by the ministry, wanted Persebaya Surabaya and Arema Indonesia teams blocked from playing but PSSI resisted.
The Indonesian government has accepted responsibility for the ban but said it will continue to work to overhaul the competition.
FIFA takes a dim view of government interference in football affairs and the AFC said the bans would extend from the playing pitch to develop programmes.
"As long as the PSSI is suspended, Indonesian football will also not be able benefit from any AFC and FIFA development programmes," the AFC said in a statement.
"PSSI officials are not allowed to participate in any AFC or FIFA training courses, seminars or workshops."
(Reporting by Julian Linden; Editing by Peter Rutherford)
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