"This is a real honor, not just for me and Heath but for all of you, that you picked this movie and this kiss over all the other ones," Gyllenhaal said. (He and Ledger beat out Brad Pitt and Angelina Jolie in Mr. & Mrs. Smith and Rosario Dawson and Clive Owen in Sin City, among others.)
The ceremony, taped at the Sony Studios in Los Angeles and hosted by Jessica Alba, will air Thursday on MTV.
The night's big winner was Owen Wilson and Vince Vaughn's Wedding Crashers, which won best picture, best on-screen team and best breakthrough performance by Isla Fisher.
Will Ferrell, presenting Jim Carrey with a lifetime achievement award, said, "This man's versatility makes Thomas Jefferson look like a big fat idiot."
Accepting the best comedic performance award for The 40-Year Old Virgin, Steve Carrell thanked "Gandhi and the Dalai Lama," adding, "If I had any familiarity with your teachings, I would not be the person I am today."
For her part, Alba, who won sexiest performance for Sin City, thanked "all the perverts who voted for me," but continued, "Thank you to the fans. I do movies for you. Practice safe sex and drive hybrids if you can."