The Youth and Sports ministry halted the league and suspended the PSSI after the body failed to follow its recommendations to ban two clubs, Arema Indonesia and Persebaya Surabaya – because of ownership issues.
The PSSI elected La Nyalla Mahmud as their new leader last week and he vowed to restart the Super League which was suspended after only two rounds.
The league already suffered a six-week delay to its start while all 18 clubs underwent reviews.
But none of Saturday's three fixtures, including Arema's home match against Pelita Bandung Raya, took place.
Two more matches are scheduled for Sunday but police have told clubs they will be refused permits to stage matches, local media reported.