Bashir's lawyers on Tuesday said the verdict had been reached on the basis of a single police report alleging a conversation between a now convicted Bali bomber and the 66-year-old cleric.
"I just filed the appeal today," Wirawan Adnan, a member of Bashir's defence team, said.
"The fundamental reason for appeal is because the court only based the decision on one piece of evidence, an interrogation report. And even the interrogation report is doubtful."
The South Jakarta Court, where the appeal was lodged, has seven days to pass it on to the Jakarta High Court, which then has 60 days to rule on the case.
The South Jakarta Court last Thursday found the 66-year-old cleric guilty of an "evil conspiracy" to commit the October 2002 Bali bombings that killed 202 people, including 88 Australian tourists.
But it ruled him not guilty of more serious charges of ordering the bombings, or involvement in the 2003 blast at the JW Marriott Hotel in Jakarta that killed 12 people.
The verdict prompted the United States and its key ally Australia, who see Bashir as the head of the al-Qaida-linked regional armed network Jemaa Islamiya, to call on Indonesia to review the sentence as too lenient.
Bashir's trial was seen by many in the international community as a test case in the world's most populous Muslim nation for judicial attempts to grapple with terrorism.