The inaugural flight was greeted by a traditional water canon salute after touchdown at Abu Dhabi International Airport.
A statement said airberlin would operate the new flights in conjunction with Etihad Airways.
This follows the recent announcement that the national flag carrier of the UAE would become airberlin's largest single shareholder.
Using an Airbus A330-200 aircraft, airberlin will operate four flights a week (Tuesday, Thursday, Friday and Sunday) between the two capital cities.
Addressing guests at Berlin Tegal airport prior to boarding inaugural flight AB7494, airberlin Chief Executive Officer Hartmut Mehdorn said: "This strategic partnership with Etihad Airways not only opens up unique opportunities for the future of airberlin. It also brings a number of benefits for passengers in terms of access to new routes, including our new all-year-round direct services to Abu Dhabi.”
Mehdorn added: "The new route will allow business and leisure travelers to experience the very best of what Abu Dhabi has to offer. In addition, it is a fantastic opportunity for travelers to use the UAE hub as a convenient and accessible gateway to Asia and Australia. We look forward to working with all the various stakeholders in making this new route a success for all."
Welcoming the flight to Abu Dhabi, Etihad Airways President and Chief Executive Officer James Hogan said: "This flight marks a key milestone in our new partnership with airberlin.”
