Images taken from inside the stadium during the stampede showed police firing huge amounts of tear gas and people clambering over fences.
People were carrying injured spectators through the chaos.
Video footage circulating on social media showed people shouting obscenities at police, who were holding riot shields and wielding batons.
The stadium holds 42,000 people and authorities said it was a sell-out, Police said 3,000 people stormed the pitch.
"We would like to convey that... not all of them were anarchic. Only about 3,000 who entered the pitch," Afinta said.
Torched vehicles, including a police truck, littered the streets outside the stadium on Sunday morning. Police said 13 vehicles in total were damaged.
The Indonesian government apologized for the incident and promised to investigate the circumstances surrounding the stampede.
"This is a regrettable incident that 'injures' our football at a time when supporters can watch football matches from the stadium," Indonesian Sports and Youth Minister Zainudin Amali told broadcaster Kompas.
"We will thoroughly evaluate the organisation of the match and the attendance of supporters. Will we return to banning supporters from attending the matches? That is what we will discuss."