Israel does not have an embassy or consulate in Pakistan (nor do they in many other countries). To apply for a visa, you will need to make your application through an Israeli embassy or consulate in a different country. The linked MFA web site has a list of all the consulates worldwide.
The visa application process is mostly the same as for people of any other nationality, but all applications from Pakistani nationals must also be approved by the Israel Ministry of Foreign Affairs, which will add a significant delay to the process, (one embassy web site states it could add 30 days or more) and if you are refused, you might not be told the reason for refusal.
Pakistani passport holders who are approved for a visa will receive the visa on a separate sheet of paper, not in the passport. The visa and any entrance/exit stamps will be placed on that paper, not in your passport (though Israel has mostly stopped entry/exit stamping entirely by now). You will need to take both your passport and the paper with the visa when you travel to Israel.
Keep in mind that it is Pakistan that does not want you traveling to Israel. Israel makes its own decisions in regard to who can visit, and does not care that your passport says it is not valid for travel to Israel. This is one reason why they place the visa on a separate paper. Along the same lines, you should be careful when booking flights. If you book a single ticket from Pakistan to Israel, then the government will know that you intend to travel there.
Note that even with a visa, Pakistanis report that they typically spend several hours passing through the Israeli border and answering a large number of questions. You should be mentally prepared for this experience.