The singer, who was found dead in the bathroom of a Los Angeles hotel room in February, teamed up with Jordin Sparks for the film, and their rendition of "Celebrate" landed them the Best Gospel/Inspirational Performance at the annual prizegiving.
Taking to her Twitter page, Sparks told fans:
So happy that Celebrate won Best Gospel/Inspirational Performance at the BET Soul Train Awards!! First of many Mama Whitney!! #missyou <3— Jordin Sparks (@JordinSparks) November 26, 2012
New Edition dominated the evening - they landed the Lifetime Achievement Award and performed a set of their hits.
Accepting the award, Houston's former husband Bobby Brown said, "I wanna thank my brothers for sticking by me at all times. I wanna thank all of you for always having my back no matter what I've been through in my life. I'm still standing on my feet."
Beyonce was a double winner at the ceremony in Las Vegas. She bagged Best Dance Performance for "Love On Top" and was also named the Best R&B/Soul Female Artist, while Miguel landed the male equivalent.
Kanye West's "Mercy," which also features Big Sean, Pusha T and 2 Chainz, won Best Hip Hop Song of the Year, "Stay" by Tyrese was heralded as Song of the Year, and Album of the Year went to Frank Ocean's Channel Orange.
The evening, which also featured a performance from Stevie Wonder, included a tribute to Soul Train creator Don Cornelius, who died earlier this year, and his son Tony took to the stage to pay tribute to his father.
He told the audience, "The magnitude of creative genius can spawn a movement that lasts a lifetime and that movement was, and is, Soul Train. My father saw something that could spiritually connect everyone in the world. Uplifting our minds, our bodies and our spirits - Don Cornelius was responsible for that. He danced his own dance."
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