"Shinzo Abe, the longest serving prime minister in Japanese history, was a proud servant of the Japanese people and a true friend of the United States," Biden said in a statement on the White House website.
He also ordered flags to be flown at half mast over government buildings in the country.
Abe died in hospital after an assassination attempt was made on him during a campaign speech in the city of Nara.
Russian President Vladimir Putin also expressed condolences to the wife and mother of former Japanese Prime Minister Shinzo Abe, who died in the assassination attempt.
Russian Foreign Ministry spokeswoman Maria Zakharova said that the Russian side was stunned by the assassination attempt on former Japanese Prime Minister Shinzo Abe and considers the incident an act of terrorism.