The three -- Murugan, Santhan and Perarivalan-- lodged in Vellore Jail, were scheduled to be hanged on September 9.
Granting the interim stay, a bench comprising justices C Nagappan and M Sathayanarayanan observed there had been a delay of over 11 years in the disposal of the mercy petitions filed by the convicts to the President seeking clemency.
The matter involved a question of law, the judges said and admitted the writ petitions and issued notices to the Centre, the state and Tamil Nadu police.
Their case was taken up by senior lawyer Ram Jethmalani and others. A crowd that had gathered outside the court welcomed the court order. MDMK leader Vaiko, who strongly pleaded for the commutation of capital punishment, was also present in the court.