The country's powerful military establishment wants to try more than 100 people accused of targeting army sites during protests in support of former prime minister Imran Khan behind closed doors.
The Supreme Court in October deemed military trials unconstitutional.
But on Wednesday, following an appeal, a different bench of judges suspended the ruling pending a final decision in January, Shoaib Shaheen, a Supreme Court lawyer, told AFP after the verdict.
Military courts can resume trials but cannot issue verdicts until the final decision, he said.
Pakistan's military has directly ruled the country for roughly half of its 76-year history, and continues to exercise enormous power.
Authorities used mobile phone geo-fencing technology to track down those who police allege damaged military buildings.
Former cricketing superstar Khan enjoys enormous support in Pakistan but his campaign of defiance against the military was met with fierce backlash by authorities.
Almost the entire senior party leadership were forced underground, with many abandoning the Pakistan Tehreek-e-Insaf party.
Khan, who has been locked up since August, was also being tried in private for leaking state documents, until Islamabad High Court ordered that a retrial take place in public.
On Wednesday he was indicted again, with a fresh trial due to begin on Thursday in the presence of his lawyers, family and a few selected journalists, his party said.
Khan says the charges are designed to keep him from contesting national elections due in February.
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