The human rights group said on Wednesday in a publicly released letter to President Widodo that it has credible evidence of a range of grave violations by paramilitary police, who it alleged were responsible for 10 unlawful killings.
The police have launched an internal probe after acknowledging excessive violence by some officers that was revealed in a video showing 10 members of the paramilitary police kicking a man and beating him with rifles.
The riots erupted despite assurances by the election supervisory agency, known as Bawaslu, that there was no evidence of systematic fraud.
Independent observers have also declared the poll free and fair and an opinion poll by Saiful Mujani Research and Consulting last week showed that around 70 percent of Indonesians agree.
The authorities have blamed the unrest on several groups, claiming that many of the rioters were paid. A retired special forces general with links to Mr Prabowo was also accused of masterminding a plot to assassinate top state officials.
Both sides said that they would accept the court’s rulings and Mr Prabowo urged his followers to stay off the streets.
The two men have been bitter political rivals for years. In 2014, Mr Prabowo lost both the election and a legal appeal against a victory by Mr Widodo after the constitutional court ruled that he had failed to produce evidence of his claims of “massive, structured and systematic fraud.”