Justice Khanwilkar, part of a bench headed by Chief Justice Dipak Misra, did not give any reason for recusing himself.
The matter will now be heard before a new bench on March 28.
Bharaitya Janata Party (BJP) leader Ajay Agrawal had challenged the May 31, 2005 verdict of the Delhi High Court discharging Britain-based Hinduja brothers - Srichand, Gopichand and Prakash Hinduja - in the case of alleged corruption in the purchase of Bofors.
The Central Bureau of Investigation (CBI) told the apex court that it has also filed an appeal against the high court order on February 2.
In its plea against the 2005 high court verdict, it had cited some new facts that need to be investigated as a ground for the reopening of the Bofors case.
Though CBI cited "new facts" but it will have a difficult task in persuading the top court to entertain its plea after sitting over it for 12 long years.
Agrawal, who had contested the 2014 Lok Sabha election from Rae Bareli against then Congress President Sonia Gandhi, has been pursuing the case for over a decade in the top court. The court had asked Agrawal to satisfy it on his locus as a third party to challenge an order in a criminal case.
He had filed the appeal after the CBI had failed to challenge the high court verdict within the mandatory 90-day period.
Earlier, Attorney General K.K. Venugopal had told the government that, in his opinion, it will be faced with the difficulty in justifying the delay of over a decade in moving the top court against 2005 Delhi High Court order.
In a letter to the Secretary, Personnel, Venugopal said: "Now, more than 12 years have elapsed. Any SLP filed before the Supreme Court at this stage, in my view, is likely to be dismissed by the Court on account of the long delay itself."
However later, said sources, Venugopal gave his oral consent to the probe agency's move to challenge 2005 order.
The CBI had on January 22, 1990, registered an FIR for alleged criminal conspiracy, cheating and forgery under the provisions of Indian Penal Code (IPC) and sections of the Prevention of Corruption Act against Martin Ardbo, the then President of AB Bofors, alleged middleman Win Chadha and the Hindujas.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)