However, he was cleared of more serious charges over a bomb attack on the JW Marriott hotel in Jakarta in 2003.
Ba’asyir, who was jailed for two-and-a-half years, had denied the charges and is expected to appeal.
Australia, which lost 88 people in the Bali attacks, said the relatively lenient sentence was “disappointing”. The US agrees.
At the end of the court case, a statement read out by the five judges said Ba’asyir had not been directly involved in carrying out the Bali blasts, but had given his approval for the attacks.
Ba’asyir addressed the court after his sentence was delivered, saying: “I don’t accept this verdict. This is not justice. God protect us from evil and its allies. Please, either open their hearts or destroy them.”