Police used tear gas to disperse hundreds of people marching through the streets in Sidi Bouzid, smashing in doors of the Ennahda party headquarters and burning tires to protest the cancellation of Popular List party seats, the BBC reported.
Election officials, who announced results Thursday, said the candidate for the party, which won six electoral districts, was invalidated because of "financial irregularities."
Results showed Ennahda captured more than 41 percent of the vote, giving the party 90 seats in the 217-member parliament.
Rachid Ghannouchi, the party leader, said his government would continue with the goals of the revolution in the country that gave birth to the Arab Spring movement, saying Tunisia was "for everyone."
Election chief Kamel Jandoubi said the Congress for the Republic, the country's biggest secularist party, was the runner-up, winning 14 percent and 30 seats in parliament.
The leftist Ettakatol party placed third with nearly 10 percent and 21 seats.
Ennahda, which had been banned under the former regime, has said it plans to form a new government within a month and would model itself on the governing AK party in Turkey, another Muslim-majority country that has remained a secular state.
Some Tunisians have worried Ennahda could endanger the country's equality and social liberalism. But Ennahda has said it would not ban alcohol, stop tourists from wearing bikinis on the beaches or impose Islamic banking.
Ennahda said party co-founder Hamadi Jebali, a 62-year-old former journalist, would be the next prime minister.
The elections came after the fall in January of President Zine el-Abidine Ben Ali, who had been in power 23 years, after mass demonstrations.