"It is Anwar's last legal avenue. We are now waiting for a date for the hearing," Sankara Nair, lawyer to Anwar, told AFP after lodging the 87-point petition at the Federal Court registry on Monday.
The petition states that Court of Appeal judges, at an earlier hearing, embarked on a "decision-making process which was fatally flawed."
Anwar filed another petition on Tuesday urging the Court of Appeal to reopen his bail hearing so that fresh arguments could be presented.
Nair said it was crucial for the court to reopen the hearing since Anwar had a good chance of being set free by the Federal Court.
The Court of Appeal said in July that it would decide soon on the bail application, but last month Anwar issued a statement accusing senior judges of delaying the decision and lacking "moral courage."
Anwar, 56, has already spent four years in jail for corruption and is pressing for bail on the grounds that his final appeal against the sodomy conviction has not yet been heard.
The ex-premier has said he also wants bail so that he can undergo spinal surgery in Germany for a slipped disc, an injury he allegedly incurred during a beating he suffered shortly after being detained in 1998.
Once seen as heir to Prime Minister Mahathir Muhammad, Anwar claims he was sacked and later charged with sodomy and corruption to prevent a political challenge to Mahathir.
His trials were criticised internationally, and the United States and human rights group Amnesty International list him as a political prisoner.