But Alice O'Keeffe, chair of the judges and books editor of the Bookseller said that despite Obama's impressive sales, Normal People was the most deserving victor.
Taking factors like sales into account in the judging process meant that the Nibbies have been "accused of following everything else", O'Keeffe said, but she felt Rooney's status as a bestseller in literary fiction, a genre that has struggled with sales in recent years, had yet to be acknowledged.
For those who have been chronicling her path, it should be no wonder that her second novel, "Normal People", has been met with similar acclaim.
Receiving the award, Rooney called it "an enormous privilege and an honour", thanking librarians and booksellers in particular for their help finding her audience. I've received such enormous support and generosity from my own publisher, Faber & Faber, and also from the book-selling community generally, from libraries and librarians, and the community of people who love books.
Speaking on the matter, O'Keeffe said, "It was a really hard decision and we went back and forth for a good while, but after much discussion, we felt that Sally Rooney is such a major talent and that her "difficult second novel" was just as impressive as her debut was astonishing".
Sally, who was unable to attend the awards, was described by the judges as a "generational talent".
Obama won best memoir, non-fiction and audiobook for her reflections in Becoming, losing out on Book Of The Year to the young Irish author. Author Leïla Slimani's book Lullaby, translated by Sam Taylor, won the best debut of the year award.
The winners from each of the British Book Awards' eight categories go forward for the overall best book of the year.
David Walliams' The Ice Monster took home children's fiction book of the year, beating entries including Jacqueline Wilson's My Mum Tracy Beaker and Nigerian-American writer Tomi Adeyemi's Children of Blood and Bone.
The beloved British writer and illustrator Judith Kerr was named Illustrator of the Year.
Philip Jones, editor of The Bookseller, said: "We are delighted with all of the winners in the book and author categories this year, which show off the breadth and dynamism of United Kingdom publishing".