Lula's plans for government provided a stark contrast to Bolsonaro's four years in office, which were characterized by backsliding on environmental protections in the Amazon rainforest, looser gun laws and weaker protections for indigenous peoples and minorities.
In the ruling, head of Brazil's electoral court Alexandre de Moraes described the challenge as "offensive" to democratic norms, adding that it sought to encourage criminal and anti-democratic movements.
"I send my congratulations to Luiz Inacio Lula da Silva on his election to be the next president of Brazil following free, fair, and credible elections," Biden said in a statement.
Adding to tensions in Brazil, Bolsonaro has made baseless attacks on the integrity of Brazil's electronic voting system and suggested he may not concede if he loses.
The Joe Biden administration did not invite Cuba, Nicaragua and Venezuela to the Summit of the Americas because of their apparent lack of democracy. The same logic, however, did not extend to the Brazilian president.