It was the latest salvo in a long-running feud between the Arab broadcaster and Prime Minister Benjamin Netanyahu's government which has worsened during the war in Gaza.
Since the war began on October 7 when Hamas Palestinian militants attacked Israel, Al Jazeera has aired continuous on-the-ground reporting on the effects of Israel's military campaign.
Four Al Jazeera journalists have been killed since the war in Gaza began, and the network's office in the territory has been bombed.
Al Jazeera called the Israeli raid "a criminal act" and an attack on press freedom.
In a conversation during the raid broadcast live on the network, an Israeli soldier told Al Jazeera's West Bank bureau chief Walid al-Omari there was a court ruling to close down the office for 45 days.
"I ask you to take all the cameras and leave the office at this moment," the soldier is seen as saying in the footage.
"Targeting journalists this way always aims to erase the truth and prevent people from hearing the truth," Omari said.
The Ramallah-based Palestinian foreign ministry condemned the Israeli operation as "a flagrant violation" of press freedom.
Shuttering the Al Jazeera office "confirms the (Israeli) occupation's efforts to disrupt the work of the media in conveying the occupation's violations against the Palestinian people," said Mohammed Abu al-Rub, director of the government media office for the Palestinian Authority which has partial administrative control in the West Bank.
The Foreign Press Association in Israel and the Palestinian Territories said it was "deeply troubled by this escalation" and called on Israel to "reconsider" the move.
"Restricting foreign reporters and closing news channels signals a shift away from democratic values," the association's board said in a statement.
In April, the Israeli parliament passed a law allowing the banning of foreign media broadcasts deemed harmful to state security.
Based on this law, Israel's government on May 5 approved the decision to ban Al Jazeera from broadcasting from Israel and close its offices for an initial 45-day period, which was extended for a fourth time by a Tel Aviv court last week.
The network condemned that decision as "criminal", saying it "violates the human right to access information".
Israel's government last week announced it was revoking the press credentials of Al Jazeera journalists in the country.
The shutdown had not affected broadcasts from the West Bank or the Gaza Strip, from which Al Jazeera was still covering the Gaza war.
Al Jazeera correspondent Nida Ibrahim said the closure of the network's West Bank office "comes as no surprise" after the earlier ban on reporting from inside Israel.
"We've heard Israeli officials threatening to close down the bureau," she said on the network.
The media office of the Hamas-run government in Gaza condemned Sunday's raid, saying in a statement it was a "resounding scandal and a blatant violation of press freedom".
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