"There is no merit in the appeal. Same is dismissed," a bench comprising Justices V Gopala Gowda and C Nagappan said.
Amin, who was granted bail in the Sohrabuddin Sheikh fake encounter case, had moved the apex court against the Bombay High Court order refusing him relief in the Ishrat Jahan case.
Earlier, the CBI had not pressed its plea seeking cancellation of Amin's bail in the Sohrabuddin Sheikh case saying that the other accused in the matter have already been granted the relief.
Amin, who is also a co-accused in the Sohrabuddin fake encounter case, was arrested on April 4, 2013 in the Ishrat Jahan murder case.
He had moved the apex court against an order of Gujarat High Court dismissing bail plea.
A Gujarat lower court had rejected his bail plea on July 9, saying that the charge sheet filed by CBI could not be deemed incomplete.
It alleged that it was a joint operation of state police and Intelligence Bureau. Amin is accused of abducting Ishrat and Javed from Vasad two days prior to the killings and firing the shots during the so-called encounter.
IPS officer G L Singhal, retired DSP J G Parmar, Mehsana DySP Tarun Barot and commando Anaju Chaudhary have been granted default bail in the case by the special CBI court as the agency failed to file charge sheet within 90 days of their arrest.
