The White House called Dylan "an icon of youthful rebellion and poetic sensitivity" and said Eastwood's films and performances are "essays in individuality, hard truths and the essence of what it means to be American."
"Obviously, their careers have helped to mark the landscape of American culture for decades," Obama said noting their absence from the East Room ceremony.
Others who made the evening ceremony for arts and humanities awards, though, were no less important to the nation's cultural identity.
Soprano Jessye Norman was recognized for "broadening contemporary operatic repertoire." Maya Lin earned a medal for her architecture, including the National Vietnam Veterans Memorial in Washington. And Obama awarded composer John Williams a medal for music featured in films such as the "Star Wars" series and the soundtrack to the Olympics.
Obama also welcomed author and activist Elie Wiesel to accept an award for his work to educate the country on the Holocaust and conductor Michael Tilson Thomas for his efforts to expand audiences and the repertoire for contemporary music.
"Each has taken a different path to get here, each has made the most of different gifts, but all of them have reached the peaks of cultural achievement and all of them are a testament to the breadth and depth of the human spirit," Obama said.
Noting the country produced talents ranging from Mark Twain to Toni Morrison, John Philip Sousa to Louis Armstrong, Obama praised the United States' diversity.
"They bring us joy, they bring us understanding and insight, they bring us comfort in good times and perhaps especially in difficult times in our own lives and the life of our nation," he said.
The president shook hands and whispered in the ears of the medal recipients as he presented them with the awards. He helped William McNeill, author and University of Chicago professor emeritus, leave the stage.
He joked: "If you fall, I'm liable."
Others receiving medals: - Rita Moreno, winner of Emmy, Grammy, Oscar and Tony awards. - Kennedy speechwriter Ted Sorensen. - Milton Glaser, a designer best known for his "I Love New York" logo. - Joseph P. Riley, Jr., mayor of Charleston, S.C., who helped build historic and cultural resources in the city. - Frank Stella, an artist the White House called "one of the world's most innovative painters and sculptors." - Robert A. Caro, a two-time Pulitzer Prize winner known for his biographies of Robert Moses and President Lyndon B. Johnson. - Pulitzer Prize-winner Annette Gordon-Reed, whose research unearthed President Thomas Jefferson's relationship with his slaves, including Sally Hemings. - Historian David Levering Lewis, who won two Pulitzer Prizes for his biographies of W.E.B. Du Bois. - Philippe de Montebello, former director of the Metropolitan Museum of Art in New York. - Philanthropist Albert H. Small, whom the White House praised "for his devotion to sharing early American manuscripts with our nation's cultural and educational institutions." - Ohio's Oberlin Conservatory of Music, the country's oldest continuously operating conservatory. - New York's School of American Ballet, the dance program co-founded by George Balanchine based at the Lincoln Center.