"On behalf of the people and government of Israel I extend our deepest condolences to the American people following last night's horrific attack on the LGBT community in Orlando," he said in a statement issued in English.
"Israel stands shoulder to shoulder with the United States at this moment of tragic loss," Netanyahu added.
Two Palestinian gunmen shot dead four people at a popular Tel Aviv nightspot on Wednesday, triggering fresh Israeli restrictions on the West Bank and Gaza Strip at the start of the Muslim holy month of Ramadan.