The vampire franchise won four accolades at the star-studded ceremony at the Greek Theatre in Hollywood, including Best Fantasy Movie, while its two main lead stars Kristen Stewart and Robert Pattinson were named Best Fantasy Actor in the Female and Male categories respectively.
Their co-star Taylor Lautner won Breakout Performance Male, while Transformers 2: Revenge of the Fallen starlet Isabel Lucas was named Breakout Performance Female.
Isabels co-star Megan Fox picked up the prize for Best Sci-Fi Actress and took the opportunity to quash rumours of a rift between her and the film’s director Michael Bay.
She said: "I would like to take this moment to actually say something genuine. There have been a lot of false reports concerning how I feel about this movie and I just want to be very clear that I've always felt that I am a very ordinary part of an extraordinary film.
These movies took me out of obscurity and they gave me a career and I am completely grateful to everyone involved with this franchise."
Earlier this year, she said of the film: Unless you're a seasoned veteran, working with Michael Bay is not about an acting experience.
Other winners at the ceremony included True Blood, which was named Best TV Show, and J.J. Abrams who was handed the Best Director prize for his work on Star Trek.
Scream 2009 Awards list of winners:
Most Anticipated Fantasy Film: Alice in Wonderland
Best Sci-Fi Actress: Megan Fox, Transformers 2
Breakout Performance, Female: Isabelle Lucas, Transformers 2
Best Villain: Alexander Skarsgard, True Blood
Breakout Performance, Male: Taylor Lautner, Twilight
Best Comic Book Writer: Jeff Jones
Best Comic Book Movie: Watchmen
Rock Immortal Award: Keith Richards
Best Horror Movie: Drag Me to Hell
Best Horror Actor, Male: Stephen Moyer, True Blood
Best Horror Actor, Female: Anna Paquin, True Blood
Best Fantasy Actor, Male: Robert Pattinson, Twilight
Best Fantasy Actor, Female: Kristen Stewart, Twilight
Scream Mastermind Lifetime Achievement Award: George A. Romero
Best Director: J.J. Abrams, Star Trek
Best TV Show: True Blood
Best Fantasy Movie: Twilight
Comic-Con Icon Lifetime Achievement Award: Stan Lee
Ultimate Scream: Star Trek