The Tunis administrative court reversed the result of the vote in Medenine, some 500 kilometres (350 miles) south of the capital, giving it to Islamist Ennahda party instead of a small Arab nationalist party, the Progressive Unionist People's Movement.
The motive for the court's decision following an appeal by Ennahda was not given.
The TAP news agency said Saturday that the administrative court had received 104 appeals against the declared results, of which 61 had been dealt with and the remainder would be settled by Tuesday.
EU electoral observers Friday urged Tunisia's election commission to publish complete results from the October 23 poll "as soon as possible", citing concerns at "weaknesses" in the counting.
"The preliminary results were not fully declared on October 27," wrote the EU's election observation mission in a statement, highlighting the lack of figures for invalid or null votes in Tunisia's first free election.
It is calling for each and every polling station to release its results.
Provisional results handed victory to the moderate Islamist Ennahda, who won with 41.47 percent of the vote ahead of two left-wing parties.
The relatively smooth running of the election won praise from the international community.
However rioting broke out in Sidi Bouzid, where the north African country's revolution began, after the election commission invalidated the party list of the Popular Petition, led by wealthy businessman Hechmi Haamdi, who had been declared winner in his home town.