Additional Sessions Judge Daya Prakash sent Bhatkal and his close aide Asadullah Akhtar to judicial custody till Jan 17.
He also allowed a plea of Delhi Police seeking his voice sample.
Bhatkal's counsel, advocate M.S. Khan, has opposed the police plea seeking a voice sample, claiming that the police had already done so during his custodial interrogation.
Bhatkal and Akhtar are accused in the 2010 Jama Masjid terror attack, which came days before the Commonwealth Games here.
Police said that on Sep 19, 2010, two bikers had fired upon tourists at the gate of Jama Masjid in old Delhi area and two Taiwanese had sustained bullet injuries while a bomb was fitted in a car parked in the area. However, it was detected and defused before it could explode.
The accused were presented in court after expiry of their police custody in connection with the 2008 Delhi serial blast case. Several bomb blasts had rocked the capital city Sep 13, 2008.