The rebukes were swift from Israeli President Reuven Rivlin and Israel's Holocaust memorial.
"Whether they be individuals or organizations, party heads or heads of state, no one will ordain the Jewish people's forgiveness, nor can this be obtained through any interest," Mr Rivlin said in a statement posted on Twitter on Saturday.
"It is no one's place to decide who can be forgiven and whether there should be forgiveness for the crimes of the Holocaust," Holocaust memorial centre Yad Vashem said in a separate statement.
"Forgiveness is something personal, my speech was never meant to be used in a historical context, especially one where millions of innocent people were murdered in a cruel genocide," he said in a statement posted on the Facebook page of Israeli ambassador to Brazil, Yossi Shelley.
The far-right Bolsonaro made a solidarity visit to Israel last month during which he raised eyebrows by asserting, after a tour of the Holocaust memorial Yad Vadshem, the Nazis had been "leftists".