The apex court said in its judgement that no further custody of Dr. Khalil Chishti is required.
Chishti was held guilty in a 20-year-old murder case, and had been serving life term.
Earlier in May 2012, the Supreme Court had allowed him to visit Pakistan temporarily, but asked him to report back to it by November 1 this year.
The Supreme Court had also asked Dr. Chishti to deposit a surety sum of Rs.5 lakh with the Indian High Commission in Islamabad.
A bench of justices P Sathasivam and J Chelameswar had asked Additional Solicitor General Mohan Parasaran in May 2012 to seek necessary instructions from the Union ministries of the home affairs and the external affairs about the conditions that could be imposed on Dr Chishti, pending disposal of his appeal against his conviction.
The bench had also said Chishti was an eminent scientist of global repute and is 82 year old with no previous criminal record and the issues involved are the bilateral relations between the two countries.
The apex court had granted bail to Chishti on humanitarian grounds, considering his old age and the fact that he has been in India since 1992 after a murder case was lodged against him when he came to visit Ajmer to see his ailing mother.
Chishti had come to see his mother in 1992 when he got embroiled in a brawl, and, in the ensuing melee, one of his neighbours was shot dead while his nephew got injured.
Born in Ajmer to a prosperous family of caretakers of the Khwaja Moinuddin Chishti shrine, Chishti was studying in Pakistan at the time of partition in 1947 and chose to stay there.