The Kerryman was nominated by the Academy in the Best Supporting Actor category for the first time for his role as a brutal slave owner 12 Years A Slave.
And while his part earned him rave reviews, Leto has swept the boards this awards season for his work as a transgender AIDS victim in the Dallas Buyer's Club.
However, his co-star Lupita Nyong'o, who won the Best Supporting Actress statue thanked him for being her 'rock' during her acceptance speech.
Fassbender arrived to the ceremony with just minutes to spare, taking his mother Adele as his date.
Meanwhile, U2 shockingly lost for Best Original Song having scooped the same award at previous ceremonies.
They performed Ordinary Love from Mandela: Long Walk to Freedom on the Oscars stage, but lost out to Let It Go from animated feature Frozen.
Alfonso Cuarón’s sci-fi drama took home a staggering seven wins during Sunday night’s ceremony at the Dolby Theatre in Hollywood, including Best Directing, Cinematography, Visual Effects, Film Editing, Sound Mixing, Sound Editing and Original Score.
As well as Best Picture, Steve McQueen’s 12 Years a Slave also won in the categories for Best Adapted Screenplay and Best Actress in a Supporting Role, which went to Hollywood darling Lupita Nyong’o.
"It doesn’t escape me for one moment that so much joy in my life is due to so much pain in someone else's,” Lupita said as tears filled her eyes while accepting the award.
Addressing director Steve McQueen, she continued: “I'm certain that the dead are standing around you, and they are grateful. And so am I.”
Dallas Buyers Club was also a big winner, tying 12 Years a Slave with three awards.
Matthew McConaughey won Best Actor in a Leading Role, a category shared with Christian Bale (American Hustle), Bruce Dern (Nebraska), Leonardo DiCaprio (The Wolf of Wall Street) and Chiwetel Ejiofor (12 Years a Slave), while his co-star Jared Leto took home Best Actor in a Supporting Role, beating out Barkhad Abdi (Captain Phillips), Bradley Cooper (American Hustle), Michael Fassbender (12 Years a Slave) and Jonah Hill (The Wolf of Wall Street).
Lupita Nyong'o, best supporting actress winner for her role in "12 Years a Slave", speaks on stage at the 86th Academy Awards in Hollywood, California March 2, 2014.
Best Actress in a Leading Role went to Blue Jasmine's Cate Blanchett, who beat out Amy Adams (American Hustle), Sandra Bullock (Gravity), Judi Dench (Philomena) and Meryl Streep (August: Osage County) for the honour.
The night also included performances from several big acts, including the nominees for Best Original Song.
Pharrell took the stage early in the night, performing his latest hit single, Happy, from the Despicable Me 2 soundtrack, getting Lupita Nyong’o, Amy Adams and other stars on their feet.
Karen O from the Yeah Yeah Yeahs performed The Moon Song from the movie Her.
U2 rocked out with Ordinary Love from Mandela: Long Walk to Freedom and Idina Menzel also performed Let It Go from Best Animated Feature Film winner Frozen, which ultimately won the honour.
Pink also gave a musical tribute the late Judy Garland, while the audience gave a standing ovation to Bette Midler, who performed Wind Beneath My Wings during the Academy’s tribute to stars who passed away over the last year, including James Gandolfini, Paul Walker and Philip Seymour Hoffman.
Larry Mullen Jr, The Edge, Bono and Adam Clayton (L-R) of the band U2 pose for photographers at the 86th Academy Awards
The full list of winners for the 86th Annual Academy Awards, hosted by Ellen DeGeneres, is as follows:
Actor in a Leading Role: Matthew McConaughey - Dallas Buyers Club
Actor in a Supporting Role: Jared Leto - Dallas Buyers Club
Actress in a Leading Role: Cate Blanchett - Blue Jasmine
Actress in a Supporting Role: Lupita Nyong’o - 12 Years a Slave
Animated Feature Film: Frozen - Chris Buck, Jennifer Lee and Peter Del Vecho
Cinematography: Gravity - Emmanuel Lubezki
Costume Design: Catherine Martin - The Great Gatsby
Directing: Gravity - Alfonso Cuarón
Documentary Feature: 20 Feet from Stardom - Morgan Neville, Gil Friesen and Caitrin Rogers
Documentary Short Subject: The Lady in Number 6: Music Saved My Life - Malcolm Clarke and Nicholas Reed
Film Editing: Gravity - Alfonso Cuarón and Mark Sanger
Foreign Language Film: The Great Beauty - Italy
Makeup and Hairstyling: Adruitha Lee and Robin Mathews - Dallas Buyers Club
Music (Original Score): Gravity - Steven Price
Music (Original Song): Let It Go – Frozen; Music and Lyric by Kristen Anderson-Lopez and Robert Lopez
Best Picture: 12 Years a Slave - Brad Pitt, Dede Gardner, Jeremy Kleiner, Steve McQueen and Anthony Katagas, Producers
Production Design: The Great Gatsby - Production Design: Catherine Martin; Set Decoration: Beverley Dunn
Short Film (Animated): Mr. Hublot - Laurent Witz and Alexandre Espigares
Short Film (Live Action): Helium - Anders Walter and Kim Magnusson
Sound Editing: Gravity - Glenn Freemantle
Sound Mixing: Gravity - Skip Lievsay, Niv Adiri, Christopher Benstead and Chris Munro
Visual Effects: Gravity - Tim Webber, Chris Lawrence, David Shirk and Neil Corbould
Writing (Adapted Screenplay): 12 Years a Slave - Screenplay by John Ridley
Writing (Original Screenplay): Her - Written by Spike Jonze
Cate Blanchett speaks on stage after she won best actress for her work in 'Blue Jasmine" at the 86th Academy Awards in Hollywood, California March 2, 2014.