In July, Netanyahu announced that he was working to shut down the network which he accuses of stoking tensions and inciting violence in Israel, particularly at the al-Aqsa mosque where six Palestinians and five Israelis, including two police officers, have been killed in recent clashes.
Israeli officials have long accused Al-Jazeera of showing bias against the Jewish state. Netanyahu tweeted his congratulations to Kara "who on my instructions took concrete steps to end Al-Jazeera's incitement" in Israel.
The minister accused the network of "supporting terrorism", Reuters reported.More news: Trump says Foxconn CEO may invest $30B
During a press conference, Israeli Communications Minister Ayoub Kara announced his intentions to limit Qatari-owned Al Jazeera's activity within Israel.
Protests erupted at the contentious site, known to Muslims as Haram al-Sharif (Noble Sanctuary), after Israel last month installed new security measures including metal detectors, following the killing of two Israeli policemen by three Israeli Arab attackers who shot them using weapons smuggled onto the holy site.
As the Guardian noted, Al Jazeera has faced crackdowns in Jordan, Saudi Arabia, the United Arab Emirates, Egypt and Bahrain, with the latter four countries blocking its channel and "affiliate sites". He said "Therefore, I have contacted the security echelon and have requested a professional opinion regarding the Al-Jazeera network". It also was the first Arab-owned news outlet to host Israeli officials and commentators, which some analysts note coincided with Qatar's ties with Israel at the time.
Mr Kara, of Prime Minister Benjamin Netanyahu's Likud party, said: 'Lately, nearly all countries in our region determined that Al Jazeera supports terrorism, supports religious radicalisation.More news: Oxford University worker in murder manhunt
The Foreign Press Association, which represents journalists covering Israel and the Palestinian territories for global news organizations, said the move "is certainly a cause for concern".
"Israel claims that it is the only democratic State in the Middle East and boast about it, but it follows, by its decision, that of dictatorial countries that do not recognize freedom of expression and freedom of information", stressed the head of Al-Jazeera.
The network's offices in the Palestinian territories of Gaza and the West Bank city of Ramallah would not be affected.More news: Government pledges €78m to help attract European Medicines Agency to Dublin