The music superstar received the accolade for the third time and is the first posthumous winner in the Brits history.
Bowie, who died of cancer in January last year aged 69, received the Outstanding Contribution to British Music award in 1996.
His final album, Blackstar was released just two days before his death.
Bowie beat grime artists Skepta and Kano, singer-songwriter Michael Kiwanuka and comeback star Craig David to the prize.
Actor Michael C Hall, who starred in Bowie’s Lazarus musical, collected the award and paid tribute to the singer.
He said: “If David Bowie could be here tonight, he probably wouldn’t be here tonight.
“But since he can’t be here tonight, I’m here on his behalf, on behalf of his family, to accept this testament to a man beholden to nothing but his own boundless imagination and daring whose ever-expanding artistic vitality simultaneously soothes us and astonishes us.”
Later, Bowie’s son, film-maker Duncan Jones, collected the late singer’s award for Best Album for Blackstar.
At the start of the night, Aberdeenshire singer Emeli Sande collected the prize for best British Female Solo Artist. She thanked her team and her fans for “allowing me to make the music I wanted to make and allowing me to express what I felt was important”.
It is the fourth Brit award for the singer. She also performed Hurts from her most recent album.
Meanwhile, indie-pop group The 1975 were named best British Group. The Manchester-formed band beat Radiohead, Bastille, Little Mix and Biffy Clyro to win their first Brit Award. However, Little Mix won best British Single with Shout Out To My Ex
Katy Perry gave a politically-charged performance, with Prime Minister Theresa May and US president Donald Trump represented by skeleton puppets holding hands.
Beyonce won the best International Female Solo Artist award, and Drake took the best International Male Artist. Adele was named Best Global Artist.
The ceremony also took time to remember some of the music stars who died in 2016, including George Michael, Prince and Leonard Cohen.
Michael, who died on Christmas Day, was remembered with a tearful tribute from his former Wham! bandmates Andrew Ridgeley and collaborators Pepsi and Shirlie. Chris Martin then offered a haunting rendition of Michael’s A Different Corner which featured a recorded performance from the late popstar.
On the screen behind the stage, home videos and interview clips of the Careless Whisper singer played.