The court said the ruling addressed a legal shortfall that failed to protect the LGBT+ community, and now frames homophobia and transphobia as crimes within Brazil’s law against racism.
Offenders could now face prison sentences of up to five years.
According to the rights group the Grupo Gay da Bahia, 420 LGBT+ people were killed across Brazil in 2018, while at least 141 have been killed so far this year.
Brazil also leads the world in transgender homicides with 171 in 2017, according to the organisation Transgender Europe. Someone is killed in a homophobic attack here every 16 hours.
“In a discriminatory society like the one we live in, the homosexual is different and the transsexual is different,” said Justice Carmen Lucia.
“Every preconception is violence, but some impose more suffering than others.”
The supreme court’s intention had already been voiced in late May after six of the 11 judges had voted in favour of the measure, but was suspended until the other judges voted.
The final votes came in on Thursday, making the ruling official with a tally of eight votes in favour and three against.
The president has a history of homophobic, transphobic and racist remarks, having in the past bragged that he was “homophobic, and very proud” and that he’d rather have a dead son than a homosexual son.
In late April, he caused outrage saying Brazil should not be “the country of gay tourism”.
As Mr Bolsonaro campaigned last year, reports of crimes against LGBT+ people tripled.
Brazil had already legalised same-sex marriage, along with Argentina, Colombia and Uruguay. On Wednesday, Ecuador became the latest South American country to join when its highest court approved same-sex marriage in a landmark ruling for the country.
Additional reporting by AP.
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