The PSSI were fined $10,000 (£6,600) after fans ignited firecrackers and threw water bottles during Indonesia's March 23 Asian Cup home qualifier against Saudi Arabia, with the additional $5,000 (£3,300) a result of similar incidents during four matches last year.
Indonesia will also have to play a match behind closed doors if the problem reoccurs in the next two years, the Asian Football Confederation said.
Saudi Arabia beat Indonesia 2-1 to lead Group C, which also features Iraq and China, with two wins from two matches. The southeast Asians are bottom after two defeats.
The top two teams from each of the five qualifying groups and the best third-placed team will join defending champions Japan, hosts Australia, South Korea and North Korea at the next edition of the tournament in 2015.
The AFC also handed a $5,000 (£3,300) fine to Brunei, who pulled out of the AFC Challenge Cup at the last moment citing "unavoidable circumstances."
The AFC also reminded Brunei to plan better in future.