"Accused no. 8 (Abdul Wahid) is found not guilty of having committed any offences with which he is charged", special MCOCA court judge Yatin D Shinde had observed while acquitted him yesterday.
In its verdict, the court had held 12 other accused guilty of various charges.
Arguments for the quantum of sentence are likely to begin on Monday.
Shaikh came out of the jail at around 2 PM with moist eyes and was welcomed by his family members.
Seven RDX bombs had ripped through the first class compartments of as many local trains on western line on July 11, 2006, killing 188 people and injuring 829.
The blasts had occurred within a span of 10 minutes between suburban Khar Road-Santacruz, Bandra-Khar Road, Jogeshwari-Mahim junction, Mira Road- Bhayander, Matunga- Mahim junction and Borivali railway stations.