Nolan had been favored to win the Oscar after earning best director awards at the Golden Globes, BAFTA, Critics Choice and the Directors Guild of America this year.
In his acceptance speech, Nolan thanked Universal and its executive Donna Langley, who made a big bet on the film, and also praised his cast and his family.
Nolan noted that movies are just a little bit over 100 years old and thanked the Academy for the honor.
"We don't know where this incredible journey is going from here," Nolan said. "But to know that you think I am a meaningful part of it means the world to me."
Nolan also wrote the screenplay for "Oppenheimer" and produced the film with his wife Emma Thomas. The film received 13 Oscar nominations, including best picture and best actor for Cillian Murphy, who played J. Robert Openheimer, known as "the father of the atomic bomb."
"Oppenheimer's story is one of the most dramatic that I know of and there are many, many aspects to what makes it so compelling," Nolan told Reuters before the film's premiere last summer.
Oppenheimer headed the secret Los Alamos Laboratory, established under President Franklin D. Roosevelt as part of the Manhattan Project to build the first atomic bomb. He oversaw the first atomic bomb detonation in the New Mexico desert, code-named "Trinity," before the weapons were used in the bombings of Japanese cities Hiroshima and Nagasaki.
The film has earned more than $957 million at the global box office.
Nolan is known for his cerebral films and was first nominated for an Oscar for screenwriting in 2002 for "Memento," which he also directed. He was nominated for best director in 2019 for World War Two movie "Dunkirk."
