His spokeswoman said in a statement that the man who was once first in line to the throne of the former Austro-Hungarian empire which covered most of central Europe died at his home in Bavaria.
Born in 1912, Habsburg was forced to flee into exile when the empire collapsed in 1919. He returned as a young adult only to be chased out again by the Nazi regime, which he had publicly opposed.
In exile, the man also known as Archduke Otto of Austria embarked on a distinguished career as a politician.
An ardent anti-Communist and devout Christian, he spent two decades as a member of the European Parliament for Germany's Christian Social Union of Bavaria and became one of the most vocal proponents of the former eastern bloc's integration into the European Union.
His spokeswoman said the funeral will taker place in Vienna on July 16.