Left on the outside in the Best Picture race were Todd Haynes' romance Carol (which fared better in acting nominations for Cate Blanchett and Rooney Mara) and the N.W.A biopic Straight Outta Compton (which landed a nod for original screenplay).
The miss for Carol, considered an shoo-in, meant usual Oscar heavyweight Harvey Weinstein won't have a horse in the Best Picture race for the first time since 2007.
Though some fans had hoped for a better showing, the box-office behemoth Star Wars: The Force Awakens also failed to land a Best Picture nomination.
Netflix, which has previously scored nominations for documentaries, fell short in its first bid for fiction film nods. Its first original feature, Beasts of No Nation, was shut out.
In the acting department, notably omitted was Idris Elba for Beasts of No Nation. Elba had 6-to-1 odds of taking home the Oscar, according to FiveThirtyEight, so his was arguably the biggest snub of all. Michael Keaton also failed to earn a nod for his role in Spotlight and he was considered to be a more likely nominee than either Ruffalo, Hardy or Bale.
Also left out were Benicio Del Toro for Sicario, Michael Shannon for 99 Homes and Jacob Tremblay for Room.
Johnny Depp's transformation into gangster James "Whitey" Bulger in Black Mass generated Oscar buzz but no nomination, and it's possible lukewarm reviews of the film led to Will Smith being left off the list for Concussion.
Sylvester Stallone may have earned a nomination for his reprisal of Rocky Balboa in Creed, but star Michael B. Jordan's performance did not.
Oscar darling Helen Mirren was also snubbed in her bid for a Best Supporting Actress nod for her part in Trumbo, as was Kristen Stewart for her Cesar Award (the French equivalent of Oscar)-winning role in Clouds of Sils Maria.
Ridley Scott's sci-fi epic The Martian landed seven nominations, including Best Picture and Best Actor for Matt Damon, but, surprisingly, no Best Director nod for Scott.
Aaron Sorkin won the Golden Globe for writing Steve Jobs, but he won't be competing for an Academy Award.
Finally, The Good Dinosaur was considered a lock for a Best Animated Feature nomination, but the Disney-Pixar offering fell short.
The Associated Press contributed to this report.
The Walt Disney Company is the parent company of Pixar Animation, Lucasfilm and this station.