He narrowly lost to the leftist former leader, Luiz Inacio Lula da Silva, and his Liberal Party (PL) claimed without evidence that voting machines were compromised.
The court said the complaint was made "in bad faith" and fined the party 22.9m reais (£3.5m; $4.3m).
Lula takes office on 1 January.
Superior Electoral Court (TSE) President Alexandre de Moraes said the PL complaint was "offensive to democratic norms" and had sought to "encourage criminal and anti-democratic movements".
Lula's victory - with 50.9% to Mr Bolsonaro's 49.1% - has been ratified by the TSE.
Mr Bolsonaro has previously claimed that Brazil's electronic voting system is not fraud-proof.
He has still not conceded defeat, but has given the go-ahead for a presidential transition. He stepped away from the public gaze after losing the election on 30 October.
Immediately after Lula's win was declared, many lorry drivers supporting Mr Bolsonaro erected roadblocks and there were scuffles with police. But Mr Bolsonaro later told them that blocking roads was not a part of "legitimate" protests.
Some of his followers have continued demonstrating outside military barracks, urging a military intervention to prevent Lula taking office.Lula, who previously served as president from 2003 to 2010, is now 77 and will become the oldest person to assume the post.
His victory was a stunning comeback for a politician who could not run in the last presidential election in 2018 because he was in jail and barred from public office. But his conviction for corruption was later annulled.
Mr Bolsonaro, a former army captain, drew much support from evangelical Christians and other conservatives anxious to protect family values. But his tenure also saw accelerated deforestation of the Amazon and growing inequality.