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In a 10-minute speech at the end of the almost three-hour ceremony, Madonna recalled her early days as an aspiring singer and dancer, including one audition where she performed an a cappella version of Franklin's iconic "(You Make Me Feel Like) A Natural Woman."
It resulted in her landing a singing job in Paris but Madonna threw that in to return to the U.S. to learn how to play guitar. She went on to become one of the world's biggest pop stars.
"None of this would have happened without our lady of soul," Madonna said. "She led me to where I am today and I know she influenced so many people in this room tonight. I want to thank you Aretha for empowering all of us. R.E.S.P.E.C.T. Long live the queen."
MTV also played a brief clip of Franklin from early in her career.
Viewers took to Twitter to criticize Madonna and MTV for the speech, saying it was self-indulgent and did not focus enough on Franklin.
"The Aretha Franklin tribute is Madonna talking about herself at great length?" author Michael Arceneaux tweeted.
Others questioned why Madonna was chosen to deliver Franklin's tribute over artists who were more closely associated with her.
Her death last week brought tributes ranging from Elton John to Carole King, Barbara Streisand and Lionel Richie, as well as former President Barack Obama.
Meanwhile, Cuban-born Camila Cabello beat out heavy hitters Beyonce, Bruno Mars and Drake to take home the two top prizes at the VMAs.
Cabello, 21, was chosen artist of the year and won video of the year for her Latin-flavored hit "Havana," while rapper Cardi B picked up wins for best new artist and song of summer for her dance hit "I Like It" with J Balvin and Bad Bunny.
"I can't believe this is for me," said Cabello, who split from girl group Fifth Harmony in late 2016 to launch a solo career.
New York rapper Cardi B, 25, made her first public appearance since giving birth to her first child in July. But the feisty "Bodak Yellow" singer failed to make good on her leading 10 nominations going into the show as fans spread their votes far and wide.
"A couple of months ago people were saying, you're gambling your career by having a baby," Cardi B said. "I had a baby ... and now I'm still winning awards."
The biggest winner of the night was Childish Gambino, the music stage name of actor Donald Glover, who came away with three for his hard-hitting video "This Is America" about black identity and police brutality.
But the trophies were mostly in technical categories, including choreography and direction.
Beyonce and Jay-Z's much talked-about "APES**T," which was shot inside the Louvre in Paris against the backdrop of some of the world's most famous art works, won just two of its eight nominations.
Canadian rapper Drake, one of the most popular artists in terms of sales and streaming, came away empty-handed, as did multiple Grammy winner Bruno Mars.
Neither Mars, Drake, Gambino, Beyonce nor Jay-Z attended the awards show in New York City, which featured performances by Ariana Grande — who won best pop video for "No Tears Left to Cry" — Nicki Minaj, Aerosmith, Shawn Mendes and Travis Scott.
Jennifer Lopez brought the audience to its feet with a song and dance medley of her biggest hits as she was presented with the annual Vanguard Award, named after Michael Jackson, recognizing her 20 years in show business.
"It's been an incredible journey of dreaming my wildest dreams and then watching them come true," said Lopez.
The VMAs have a reputation for irreverence and provocative stunts but, aside from a segment on U.S. President Donald Trump's controversial immigration policies, there were few surprises.
Rapper Logic was joined onstage by dozens of immigrant children and their families wearing white T-shirts saying "We are all human beings," for a performance of his song "One Day."
The song is a protest against the policy that saw thousands of immigrant children separated from their parents after crossing the southern border with Mexico.