The 38-year-old is thought to have planned the massive truck bombings in Nairobi and Dar es Salaam that killed 224 people in 1998 and had a $5 million bounty on his head, making him Africa's most wanted man.
In addition to a South African passport Fazul was carrying evidence clearly linking him to Somali Islamist insurgents, the government said.
He "was carrying ... documents with the signature of Sheikh Hassan Dahir Aweys, one of the top leaders of Al-Shabab, an affiliate of Al-Qaeda," it said.
Sheikh Hassan Dahir Aweys
A Somali source said the South African passport found on Fazul was in the name of Daniel Robinson and gave his date of birth as 1971.
The passport, issued April 13, 2009, indicated that its bearer left South Africa for Tanzania on March 19 and was granted a visa there. The Tanzanian visa was the only one in the passport.