Wonder was a surprise performer at the show in Las Vegas when he joined Madonna on stage for a rendition of ‘Purple Rain’ following Prince’s sudden death last month.
The duet came after Madonna, wearing a purple sequinned suit and holding a cane and cross symbols, sang ‘Nothing Compares 2 U’.
“Thank you Prince Rogers Nelson for all you have given us,” she said following her performance.
Organisers defended their decision to choose Madonna to honour Prince after an online petition calling for other artists to be involved in the homage attracted more than 8,000 signatures.
The Weeknd hailed Prince as his “inspiration” after he was named the Top Hot 100 Artist, as the Canadian singer became the biggest winner of the night, collecting eight awards.
Adele, who did not attend the ceremony as she continues her world tour, won five awards including Top Artist as she beat Justin Bieber, Drake, Taylor Swift and The Weeknd in the category.
She also won prizes for Top Female Artist, Top Billboard 200 Artist, Top Selling Song for ‘Hello’ and Top Billboard 200 Album award for 25.
Celine Dion broke down in tears as her son presented her with the Icon Award, Billboard’s lifetime achievement honour, after a traumatic start to 2016 for the singer.
She sang Queen’s ‘The Show Must Go On’ in her first televised performance since her husband, Rene Angelil, and brother, Daniel, died from cancer just days apart in January.
Kesha received a standing ovation for her rendition of Bob Dylan’s ‘It Ain’t Me Babe’ after her former producer’s record label had initially refused to approve the performance.
Britney Spears opened the show after receiving the Billboard Millennium Award for “career achievements and influence on the music industry”.
Wearing a red sequinned bra and red knee-length boots, Spears performed a medley of her hits including ‘Womaniser’, ‘I’m A Slave 4 U’ and ‘Toxic’.
She is only the third person to receive the award after Beyoncé in 2011 and Whitney Houston in 2012.