Obama also called Rudd's predecessor, Julia Gillard, who resigned the prime minister's post last week after losing a party leadership vote to Rudd.
Obama made both calls from Air Force One as he traveled from South Africa to Tanzania.
The White House said Obama expressed confidence that the U.S. and Australia would continue to work closely on international and regional issues. Obama and Rudd also discussed the importance of completing the Trans-Pacific Partnership trade agreement.
Obama developed a friendly relationship with Gillard, who was his host during his 2011 trip to Australia.
The White House said Obama thanked her for her warm friendship and wished her well.