The network, which Israel has called a threat to its security, broadcast the operation live.
Israeli forces have raided the offices of news broadcaster Al Jazeera in Ramallah, in the occupied West Bank, and ordered it to close for an initial period of 45 days.
Armed and masked Israeli soldiers entered the building early on Sunday during a live broadcast.
Viewers watched as the troops handed the closure order to the network’s West Bank bureau chief Walid al-Omari who read it out live on air.
Israel raided Al Jazeera's offices in Nazareth and occupied East Jerusalem in May having described the Qatar-based broadcaster as a threat to national security.“Targeting journalists this way always aims to erase the truth and prevent people from hearing the truth,” Omari said in comments reported by his employer.
The soldiers confiscated the last microphone and camera off the street outside and forced Omari out of the office, Al Jazeera journalist Mohammad Alsaafin said.
Posting about the raid on social media, Alsaafin said the troops also pulled down a poster of Shireen Abu Aqla - an Al Jazeera reporter who was killed while covering a raid by Israeli forces in the West Bank.
The network and witnesses at the time said the Palestinian-American reporter was shot by Israeli forces. Israel initially argued she had been shot by a Palestinian, however months later concluded there was a "high probability" that one of its soldiers killed her.
Relations between the Qatari-owned broadcaster and the Israeli government have long been tense but have worsened dramatically following the outbreak of war in Gaza.
With foreign journalists banned from entering the strip, Al Jazeera staff based in the area have been some of the only reporters able to cover the war on the ground.
Israel has repeatedly branded the network a terrorist mouthpiece, an accusation Al Jazeera has denied.
In April, the Israeli parliament passed a law giving the government power to temporarily close foreign broadcasters considered a threat to national security during the war.
A ban would be in place for a period of 45 days at a time, as seen in Sunday's raid, and can be renewed.
In early May, the Al Jazeera offices in Nazareth and occupied East Jerusalem were subject to separate raids.
Israel is yet to comment on Sunday's operation.
<p>The US president has been vague about what victory looks like for both allies, leaving their leaders to pursue their own agenda</p>