Maideen was one of five accused, who were at large since the blasts occurred on February 14, 1998 during a visit by BJP leader L K Advani.
The explosions claimed 58 lives and injured 250 people. Maideen, arrested later on the charge of murdering three Hindu Munnai leaders in Melapalayam in Tirunelveli district, was acquitted by a fast track court on Wednesday.
On learning of his acquittal, a special investigation team probing the blasts arrested him from Melapalayam after executing a non-bailable warrant that was pending against him, police said.
He was brought to Coimbatore and produced in the judicial magistrate's court, which remanded him to custody.