The decision by the general court in Jeddah came less than nine months after the editor of the "Free Saudi Liberals" website, Raif Badawi, was sentenced to seven years in jail and 600 lashes for setting up a forum that violated Islamic values.
"By order of the court, this network has been closed permanently," said an message on Badawi's website humanf.org.
International human rights groups and activists inside Saudi Arabia say the kingdom's authorities are seeking to curb political, religious and social dissent in the birthplace of Islam. The government denies there is a crackdown.
Saudi news websites akhbar24.com and sabq.org said that the Jeddah court's ruling was due to "the subjects and comments that had been published in the past in violation of the teachings of the religion (Islam) and which had stirred controversy."
A Justice Ministry spokesman said he was checking the report.
Saudi media last July reported that a court found Badawi, who was arrested in June 2012, guilty of setting up an internet forum that violated Islamic values and propagated liberal thought. It also convicted him of disobeying his father - a crime in the conservative kingdom.
Badawi's website had included articles that were critical of senior religious figures such as the Grand Mufti, according to Human Rights Watch.
Judges base their decisions on their own interpretation of religious law rather than on a written legal code or on precedent.
King Abdullah, Saudi Arabia's ruler, has pushed for reforms to the legal system, including improved training for judges and the introduction of precedent to standardise verdicts and make courts more transparent.
However, Saudi lawyers say that conservatives in the Justice Ministry and the judiciary have resisted implementing many of the changes announced in 2007.