Bolsonaro is currently under house arrest in Brasilia. He can appeal the sentence.
Four of the five justices reviewing the case in the panel found the far-right politician guilty on five counts.
US President Donald Trump said hours later that he was suprised by the conviction. Speaking to reporters as he departed the White House, he said he always found Bolsonaro to be "outstanding."
The conviction, he added, is "very bad for Brazil."
Trump has previously called the case against Bolsonaro a "witch hunt" and slammed Brazil with tariff hikes, sanctions against the presiding judge, and the revocation of visas for most members of Brazil's high court.
The latest to rule were Cármen Lúcia and Cristiano Zanin on Thursday, a day after another justice, Luiz Fux, disagreed and voted to acquit the ex-president of all charges.
Lawyers for Bolsonaro have said they will appeal the verdict to the full Supreme Court of 11 justices.
Justice Lúcia said she was convinced by the evidence the Attorney General's Office presented against the former president. "He is the instigator, the leader of an organisation that orchestrated every possible move to maintain or seize power," she said.
The trial has divided Brazil, with people backing the process against the former president, while others still support him. Some have taken to the streets to back the far-right leader who contends he is being politically persecuted.
Observers say the US might announce new sanctions against Brazil after the trial, further straining their fragile diplomatic relations.
Justice Alexandre de Moraes, who is overseeing the case, said Tuesday that Bolsonaro was the leader of a coup plot and of a criminal organisation, and voted in favor of convicting him.
Fux, in his dissenting opinion on Wednesday, disagreed with de Moraes and the other two justices.
"No one can be punished for cogitation," Fux said. "A coup d'état does not result from isolated acts or individual demonstrations lacking coordination, but rather from the actions of organised groups, equipped with resources and strategic capacity to confront and replace the incumbent power."
Prosecutors charged Bolsonaro with counts including attempting to stage a coup, being part of an armed criminal organisation, attempted violent abolition of the democratic rule of law, as well as being implicated in violence and posing a serious threat to the state's assets and listed heritage.
"Bolsonaro attempted a coup in this country, and there is hundreds of pieces of evidence," Lula said early Thursday in an interview with local TV Band, ahead of the trial.
