They were joined by Redman, Fetty Wap and Wyclef Jean for a New Jersey tribute.
Other winners included Taylor Swift, who used her speech to call out the White House.
Queen Latifah, Redman, Wyclef Jean, Naughty By Nature will all take the stage.
Fans launched several petitions urging MTV to honor the rapper and producer.
Monday night’s broadcast suffered double-digit declines from a year ago.
Furious fans say Madonna showed no respect to the Queen of Soul.
The Carters (aka Beyoncé and JAY-Z) followed with eight nominations
The union’s current contract with MTV parent company, Viacom, expires on Aug. 13.