The move directly affects six militants who were facing imminently execution.
In December Pakistan ended a seven-year moratorium on executions, after militants killed more than 150 pupils and staff at a school in Peshawar.
Since then about 60 death-row inmates have been executed on the orders of civilian courts.
More than 8,000 people have been sentenced to death in Pakistan, human rights groups say.
In March the government announced that all of those who had exhausted the appeals process and pleas for clemency would be executed.
But on Thursday, a 17-judge panel headed by Chief Justice Nasir-ul-Mulk suspended executions carried out by the military, after the Supreme Court Bar Association challenged the constitutional amendment that created the tribunals.
It said that the tribunals would not be allowed to handle terror cases, which can carry the death penalty, until it makes it final ruling.
It is not clear when the court will do so, but it has directed the attorney general to file a reply in the cases of condemned prisoners by 22 April.
Human rights lawyer Asma Jehangir has criticised the secrecy of the military tribunals, arguing that defendants are given few details of the alleged offences.
Senior lawyer and retired Colonel Inam-ur-Rehman - who has defended cases before the military courts - told AFP that Thursday's ruling was a "great achievement".
"It shows that the judiciary is performing its role independently and no parallel judiciary can be allowed to work in the country," he said.
Pakistan's Supreme Court has suspended death sentences passed by controversial new military tribunals, until it rules on the legality of the sentences.