The first magistrates court in Ankara threw out the appeal filed earlier this week by the Wikimedia Foundation, which owns the domain name for Wikipedia, the state-run Anadolu news agency said.
The ban had been imposed on Saturday by Turkey's Information and Communication Technologies Authority (BTK) and had remained in place after being backed up by a court order earlier this week.
Turkish officials have said that the ban was needed as Wikipedia had failed to remove content deemed to be false from its pages that linked Turkey with terror groups.
There have also been questions why Turkey had to ban the entire website in all languages as its objections reportedly related only two pages in the English version.
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BTK head Omer Fatih Sayan said earlier this week that the ban would only be lifted when the judiciary's decisions were implemented and the pages removed.
Istanbul municipality officials on Tuesday also removed Wikipedia founder Jimmy Wales from the guest list of the World Cities Expo, a major international conference to be held in the city on May 15-18.