A bench of justices P Sathasivam and BS Chauhan directed the duo to surrender by April 30.
If they fail to surrender, the Central Bureau of Investigation (CBI), which is probing the scam, has been directed to arrest them.
Gopalakrishnan and Gupta were granted bail by the Andhra Pradesh High Court in June 2010.
The CBI had later challenged the bail in the apex court, which Thursday upheld its plea on the basis of the investigating body's charge-sheet.