“Rivalry is only 90 minutes. After that we’re brothers. Humanity above all else,” Persebaya wrote on their official Instagram account.
The match was guarded by hundreds of security forces around the stadium and only a few officials linked to the clubs were allowed inside.
There were no reports of fan trouble outside the stadium.
The game was set to take place in March but was postponed by officials who recommended it take place outside of Persebaya’s hometown in East Java because of risks including crowd trouble.
Police described the Oct 1 pitch invasion – after Arema lost 3-2 – as a riot and said two officers were killed, but survivors and investigators said the police used excessive force.
Five Indonesian men, including three police officers, were charged with negligence after the tragedy and remain on trial.
The tragedy forced Indonesian officials and fans to confront failings in every aspect of the domestic game, which has been blighted for years by shaky infrastructure, mismanagement and violence.
Last month Muslim-majority Indonesia lost the right to host the U20 World Cup because of opposition from two prominent governors to Israel’s participation.