The CBI had filed an application in the court seeking a 14-day custody of Pandey.
Pandey finally surrendered in the court on Tuesday.
The Supreme Court on Monday rejected his anticipatory bail plea in connection with the case.
The apex court said it rejected his bail plea since he remained an absconder in the case.
Nineteen-year-old Ishrat was gunned down by the Gujarat Police along with Javed Ghulam Sheikh alias Pranesh Kumar Pillai, Amjad Ali alias Rajkumar Akbar Ali Rana and Jisan Johar Abdul Gani in Ahmedabad on June 15, 2004.
The police alleged that Ishrat and three others were Lashkar-e-Taiba (LeT) militants who conspired to assassinate Gujarat Chief Minister Narendra Modi.
--IBNS (Posted on 17-08-2013)