This meeting came after Israel and the United Arab Emirates last month signed an agreement in Washington to forge a broad new relationship.
Israeli Foreign Minister Gabi Ashkenazi and his UAE counterpart Sheikh Abdullah bin Zayed al-Nahyan began their visit to Germany with a tour of Berlin's Holocaust Memorial dedicated to Jews killed in World War Two.
As they greeted each other by touching their elbows next to the monument's maze of gravestone-like blocks, both wearing masks, a joyful Sheikh Abdullah bin Zayed al-Nahyan was heard telling his Israeli counterpart "I'm sorry that our first time, we shake this way."
German Foreign Minister Heiko Maas in a written statement on Monday evening said "it is a great honour that the Israeli and Emirati foreign ministers have chosen Berlin as the location for their historic first meeting."
A joint news conference with the German, Israeli and Emirati foreign ministers was scheduled for later on Tuesday.