The often reclusive Jackson made a surprise appearance and garnered a huge ovation as he danced briefly with the 70-year-old Brown, who also performed "It's a Man's World" and "Sex Machine."
"Nobody has influenced me more than this man right here," an emotional Jackson told the audience moments after wrapping a cape around Brown's shoulders.
Brown, a seminal figure in rock, pop and soul, is also known as "Soul Brother No. 1" and the hardest working man in show business. He is currently on a national concert tour.
The awards by BET - which, along with CBS, is a unit of Viacom - recognize people of color in music, film and sports categories. They are voted on by record label executives, news media representatives and fans.
The third annual awards show was broadcast live on the East Coast and on a taped-delayed basis on the West Coast on the Black Entertainment Television network. Actress Mo'Nique was host.
Other winners included Los Angeles R&B quartet B2K for top group and Queen Latifah for best actress. Tennis star Serena Williams beat out her sister Venus for best female athlete.
R. Kelly tied with fellow crooner Jaheim for best male R&B artist and Derek Luke was named best actor. Erykah Badu and Common won for their "Love of My Life" video and Snoop Dogg's airy pairing with Pharrell on "Beautiful" won best collaboration.
Repeat winners from last year included best female hip-hop artist Missy "Misdemeanor" Elliott, best gospel artist Yolanda Adams, best female R&B artist India.Arie and best male athlete Kobe Bryant of the Los Angeles Lakers.
A former Lakers basketball star turned business entrepreneur, Earvin "Magic" Johnson, received the humanitarian award.
Before the event, police and federal agents arrested three men and detained six others who arrived with Snoop Dogg. The rapper was not questioned, but authorities spoke with his lawyer.
Two of the three arrested were wanted on misdemeanor crimes, and another on parole violations, authorities said. The six others were armed and identified themselves as Snoop Dogg's security detail, said Joe Gordon, assistant special agent in charge for the federal Bureau of Alcohol, Tobacco, Firearms and Explosives.
They were released but Gordon said the case would be turned over to federal prosecutors and could result in charges being brought against Snoop Dogg for being a felon with armed bodyguards.