"There is a court decision to close Al Jazeera for 45 days," said an Israeli soldier to the local bureau chief Walid al-Omari during the military action, which the channel broadcast live.
The channel's employees were ordered to take their equipment and immediately leave the office.
The order is said to have been issued by the Israeli military after legal and intelligence assessments "established that the offices were used to incite terror, to support terrorist activities" and that the broadcasts endangered Israel's security, according to a statement.
Earlier this year, Al Jazeera was banned in Israel. Israel then accused the channel of spreading false content.
The channel, whose largest financier is Qatar, has rejected the accusations and condemns Israel's "criminal act" in a statement.
Furthermore, the channel believes that "the raid on the office and the seizure of our equipment is not only an attack on Al Jazeera, but a violation of press freedom and the very principles of journalism."
The channel has been covering the war between Israel and Hamas non-stop since Hamas' terrorist attack on Israel almost a year ago, and often quotes statements from Hamas and other groups that Israel considers terrorists.
The channel continues to broadcast from Amman in Jordan after the closure in Ramallah.