Instead, judges selected short story writer Saunders's first novel Lincoln in the Bardo, which takes follows United States president Abraham Lincoln as he visits the grave of his son Willie, and Auster's 4321, a novel that judges called "magisterial", about a boy called Archibald Isaac Ferguson, whose life takes four simultaneous fictional paths.
The shortlist sees three women and three men making it to the top six that include British heavyweights Paul Auster and George Saunders along with Fiona Mozley, Ali Smith, Mohsin Hamid and Emily Fridlund.
The Man Booker Prize just announced the shortlist for 2017 and it seems that there are quite a few hits and misses. Lincoln in the Bardo is short story writer George Saunders's first full-length novel.
Arundhati Roy's novel The Ministry of Utmost Happiness could not find a place on the shortlist.
The shortlisted authors each will receive 2,500 pounds and a specially bound edition of their book.
British-Pakistani author Mohsin Hamid completes the shortlist for Exit West, about the movement of large numbers of people across the globe in search of freedom.
Also left out were favourites such as Zadie Smith, Sebastian Barry and Colson Whitehead, whose speculative slavery narrative The Underground Railroad won the Pulitzer Prize for Fiction earlier this year.
"With six unique and intrepid books that collectively push against the borders of convention, this year's shortlist both acknowledges established authors and introduces new voices to the literary stage".
The victor will be announced on October 17 in London. "Playful, sincere, unsettling, fierce: here is a group of novels grown from tradition but also radical and contemporary".
He has written four novels, Moth Smoke, The Reluctant Fundamentalist, How to Get Filthy Rich in Rising Asia, and Exit West, and a book of essays, Discontent and Its Civilizations.
Last year's victor was "The Sellout by Paul Beatty", while "A Brief History of Seven Killings by Marlon James" was victorious in 2015.