Peter Dinklage was on hand to present the funnyman with the gong, poking fun at his toilet habits, before calling Ferrell "the best" at comedy.
After a look back at some of his most famous roles - including Anchorman and Elf - Will bounded on stage in a dollar-design suit to accept the accolade, giving a typically funny speech.
Ferrell screamed "Comedic Genius" at the top of his lungs, before thanking MTV for his "amazing" award.
He said: "I'm just a simple guy from California who had two basic dreams that one day, I could hopefully make people laugh and to dress myself exactly like Dennis Rodman."
Actress Aubrey Plaza then gatecrashed the stage, trying to pinch his Golden Popcorn - in a shameless stunt to promote her new movie The To Do List - but like a true professional, the actor continued on with his acceptance speech.
He then welcomed his fake family on stage, who he proceeded to thank them for their support, surprising his 'wife' Pam and renewing their wedding vows.
It later emerged that Plaza - who was holding a cup she later dropped on her way back to her seat - wasn't supposed to join the funnyman at all, and the whole back-and-forth was unscripted. Shortly after she interrupted the actor's big moment, she was asked to leave the show by producers.
You can catch all the action from the Rebel Wilson-hosted MTV Movie Awards when it hits MTV UK on April 15 @ 21:00!
Movie of the Year Django Unchained Silver Linings Playbook Ted The Avengers: WINNER! The Dark Knight Rises
Best Female Performance Anne Hathaway - Les Misérables Mila Kunis - Ted Jennifer Lawrence - Silver Linings Playbook: WINNER! Emma Watson - The Perks of Being a Wallflower Rebel Wilson - Pitch Perfect
Best Male Performance Ben Affleck - Argo Bradley Cooper - Silver Linings Playbook: WINNER! Daniel Day-Lewis - Lincoln Jamie Foxx - Django Unchained Channing Tatum - Magic Mike
Breakthrough Performance Ezra Miller - The Perks of Being a Wallflower Eddie Redmayne - Les Misérables Suraj Sharma - Life of Pi Quvenzhané Wallis - Beasts of the Southern Wild Rebel Wilson - Pitch Perfect: WINNER!
Best Scared-As-S**t Performance Jessica Chastain - Zero Dark Thirty Alexandra Daddario - Texas Chainsaw 3D Martin Freeman - The Hobbit: An Unexpected Journey Jennifer Lawrence - House at the End of the Street Suraj Sharma - Life of Pi: WINNER!
Best On-Screen Duo Leonardo DiCaprio and Samuel L. Jackson - Django Unchained Bradley Cooper and Jennifer Lawrence - Silver Linings Playbook Mark Wahlberg and Seth MacFarlane (as Ted) - Ted: WINNER! Robert Downey Jr and Mark Ruffalo - The Avengers Will Ferrell and Zach Galifianakis - The Campaign
Best Shirtless Performance Christian Bale - The Dark Knight Rises Daniel Craig - Skyfall Taylor Lautner - The Twilight Saga: Breaking Dawn - Part 2: WINNER! Seth MacFarlane (as Ted) - Ted Channing Tatum - Magic Mike
Best Fight Jamie Foxx vs Candieland Henchmen - Django Unchained Daniel Craig vs Ola Rapace - Skyfall Mark Wahlberg vs Seth MacFarlane (as Ted) - Ted Robert Downey Jr., Chris Evans, Mark Ruffalo, Chris Hemsworth, Scarlett Johansson and Jeremy Renner vs Tom Hiddleston - The Avengers: WINNER! Christian Bale vs Tom Hardy - The Dark Knight Rises
Best Kiss Kerry Washington and Jamie Foxx - Django Unchained Kara Hayward and Jared Gilman - Moonrise Kingdom Jennifer Lawrence and Bradley Cooper - Silver Linings Playbook: WINNER! Mila Kunis and Mark Wahlberg - Ted Emma Watson and Logan Lerman - The Perks of Being a Wallflower
Best 'WTF' Moment Jamie Foxx and Samuel L. Jackson, Django Unchained ('Candieland Gets Smoked'): WINNER! Denzel Washington - Flight ('Final Descent') Anna Camp - Pitch Perfect ('Hack-Appella') Javier Bardem - Skyfall ('Oops… There Goes His Face') Seth MacFarlane - Ted ('Ted Gets Saucy')
Best Hero Martin Freeman - The Hobbit: An Unexpected Journey: WINNER! Christian Bale - The Dark Knight Rises Robert Downey Jr. - The Avengers Anne Hathaway - The Dark Knight Rises Mark Ruffalo - The Avengers Kristen Stewart - Snow White and the Huntsman
Best Villain Javier Bardem - Skyfall Leonardo DiCaprio - Django Unchained Marion Cotillard - The Dark Knight Rises Tom Hardy - The Dark Knight Rises Tom Hiddleston - The Avengers: WINNER!
Best Musical Moment Anne Hathaway - Les Misérables Channing Tatum, Matt Bomer, Joe Manganiello, Kevin Nash and Adam Rodriguez - Magic Mike Anna Kendrick, Rebel Wilson, Anna Camp, Brittany Snow, Alexis Knapp, Ester Dean and Hana Mae Lee - Pitch Perfect: WINNER! Bradley Cooper and Jennifer Lawrence - Silver Linings Playbook Emma Watson, Logan Lerman and Ezra Miller - The Perks of Being a Wallflower
MTV Generation Award Jamie Foxx Comedic Genius Award Will Ferrell