Earlier on Tuesday, the court rejected Pandey's first anticipatory bail plea.
The court later heard and rejected his second plea seeking exemption from arrest for the next two days as he is filing an appeal in a higher court.
Pandey is now expected to surrender himself before the magistrate court that had issued an arrest warrant against him.
Pandey, who was an accused in the Ishrat Jahan fake encounter case, on Friday moved the Supreme Court seeking quashing of all charges against him.
On July 29, Pandey, who was to appear before a trial court in connection with the case, got himself admitted to Chandramani Hospital in Ahmedabad complaining of chest pain.
The Gujarat cop, who was an absconder in the Ishrat Jahan fake encounter case, was to appear before a Central Bureau of Investigation (CBI) court on July 29.
On July 26, the Supreme Court directed the CBI to not to arrest Pandey till July 29.
The apex court had ordered Pandey to appear before the trail court in Ahmedabad on that date.
Pandey was the Joint Commissioner Police when Ishrat was killed.
The Supreme Court had ordered that Pandey must appear before the court on July 29 which is handling the Ishrat Jahan fake encounter case, failing to which will lead to his arrest.
The CBI on July 3 submitted its first chargesheet in the 2004 Ishrat Jahan fake encounter case in the Gujarat High Court where it claimed that the teenager was not a terrorist and was killed in a fake encounter by officers of state police and Intelligence Bureau (IB).
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 06-08-2013)