The PSSI accepted the sanction, the association said on its official website on Tuesday.
"The PSSI respects the legal process and decision taken by FIFA. We will soon meet our obligation and conduct evaluation to prevent similar incident from recurrence," PSSI Secretary General Ratu Tisha Destria said.
She said the PSSI will make every effort to make the violence the last.
The association expressed hope all stakeholders to synergize to realize positive values in the football.
A few Indonesian supporters threw bottles and smoke bombs during the second round of the first home-away match between Indonesia and Malaysia of the 2022 FIFA World Cup Qualification. Following the incident, the game was stopped for 10 minutes.