Mouwafak al-Rubaie, Iraq's national security adviser, on Wednesday identified the arrested man as Yusri Fakhir Muhammad Ali, a Tunisian also known as Abu Qudama.
Al-Rubaie said the man was seriously wounded in a clash with security forces north of Baghdad a few days ago in which 15 other foreign fighters were killed. Abu Qudama has reportedly confessed to the bombing.
The national security adviser said Abu Qudama entered Iraq in November 2003.
He was part of a group including two other Iraqis and four Saudis who carried out the attack on the Askariya shrine, along with the group's leader, Haitham al-Badri, the al-Qaida leader in Salah al-Din province who al-Rubaie said masterminded the bombing.
Abu Qadama is also wanted for the murder of Atwar Bahjat, a television correspondent for Al-Arabiya news channel and former Aljazeera journalist, who was shot dead along with two of her colleagues hours after the shrine bombing, al-Rubaie added.
Al-Badri is still at large, while it is not clear whether the other group members are in custody.
"Iraqi forces ... have achieved major penetrations of al-Qaida and other terrorist groups"
Iraq's National Ssecurity Adviser
"Iraqi forces and its intelligence have achieved major penetrations of al-Qaida and other terrorist groups," al-Rubaie said.
The gang reportedly planted bombs in the 1,200-year-old Askariya mosque that exploded and obliterated its glistening golden dome, an addition completed in the 20th century.
The bombing led to violence in Iraq between the country's Sunni and Shia groups.
More than 20,000 familes were displaced from their homes, hundreds of civilians were killed and dozens of mosques belonging to both Muslim sects were damaged or destroyed.