The ruling to suspend the case until February 7 came at a brief but tense hearing marred by far-right demonstrators attacking and booing the author as he made his way into the courtroom.
The presiding judge said he wanted the Ministry of Justice to give its approval for the prosecution.
The court had ruled on December 2 that since the alleged offence was committed before Turkey amended its penal code earlier this year, Mr Pamuk should be judged under the old law, which requires a direct order from the ministry for the trial to proceed.
With no authorisation coming by the time the hearing began, the court agreed to a prosecution request to suspend the trial until the ministry decides on whether or not to try Mr Pamuk.
The ruling came despite opposition from the author’s lawyer, who asked the court to either proceed and hear his client's testimony, or drop the case altogether.
"I am sorry that I could not make (my) defence," Mr Pamuk said in a written statement after the hearing. "It is not good for Turkey or for our democracy for trials concerning freedom of thought -- which should never happen in the first place -- to be lengthy affairs."
The 53-year-old author risks six months to three years in jail for "denigrating the Turkish national identity" in remarks published in a Swiss magazine concerning the Armenian massacres during World War I.
"One million Armenians and 30,000 Kurds were killed in these lands and nobody but me dares talk about it," he told Das Magazin in February.
Turkey categorically denies Armenian accusations that up to 1.5 million of their kinsmen died in a genocide orchestrated by the Ottoman Empire between 1915 and 1917, in the dying years of its existence.
Friday's ruling drew harsh condemnation from members of the European parliament amid EU declarations that the trial is a test of freedom of speech in Turkey, which began EU membership talks in October.
"It is a bad day. The government missed the chance to cancel the case and now risks a deterioration of Turkey's standing in Europe," Camiel Eurlings, the European Parliament's rapporteur on Turkey, told journalists.
"The minister of Justice had the power to stop this case from happening. It's a disappointment that he did not," he said.
Another European MP, Joost Lagendijk, warned that the continuation of the trial would spell trouble for Turkey's hopes of joining the EU.
"If the government says at the end of the day, 'Yes, you can carry on with the trial, then Turkey is in big trouble," he told news agency AFP.
Turkey's Justice Minister Cemil Cicek, meanwhile, congratulated the court.
"This is exactly what should have happened," Mr Cicek said in Ankara, the Anatolia news agency reported.
Outside the court demonstrators chanted "Traitor," and "Sold-out intellectuals."
Several demonstrators tried to stop Mr Pamuk's car by throwing themselves on the hood while others threw eggs at people leaving the courthouse.
Police took two demonstrators into custody, the CNN-Turk news channel said.