Bolsonaro, who has in the past acknowledged that he is a homophobe, was speaking at a national convention of the evangelical Assemblies of God Madureira churches. Conservative church groups have been leading resistance to LGBT rights measures and contributed to his victory in the last presidential election.
Earlier this month, a majority of the top court's justices ruled that homophobia should be framed within the racism law until congress approves specific legislation. They argued the ruling was to address an omission that had left the LGBT community legally unprotected.
The final decision is due on June 5 after the remaining judges who have not yet voted make their decisions, but the result will not be modified.
In 2018, 420 LGBT people were killed across Brazil, according to the nonprofit Grupo Gay da Bahia.
During his 27 years in Congress and then campaigning for president, Bolsonaro, a former army captain, has repeatedly made offensive comments about gays, blacks, other minority groups and women.
He once said in an interview he would rather have a dead son than a gay son.