The singer will play to 65,000 fans at the open-air venue on 2 July, 2017. He has also announced a date for Cardiff's Principality Stadium on 30 June.
It comes a day after the star's single, Sorry, was revealed as the most-streamed video of 2016.
According to video site Vevo, the video was seen 1.8 billion times worldwide, and 87 million times in the UK.
Bieber is up for album of the year at the Grammy Awards, where he received seven nominations earlier this week.
The BST festival has gained a reputation for booking some of music's biggest stars for one-off, exclusive performances.
Last summer's festival saw Carole King play her first UK show for more than 25 years and Stevie Wonder recreating his magnum opus, Songs in the Key of Life, in full.
Bieber is not quite as elusive as those stars, having played 18 dates in the UK this year - including two headline sets at the V Festival in Chelmsford and Staffordshire.
He has gained a reputation for petulant stage behaviour - calling Instagram "the devil" and demanding his fans remain quiet in between songs.
"The screaming in these breaks has got to stop. Please and thank you," he said on stage in Manchester.
"I don't think it's necessary when I'm trying to say something and you guys are screaming."
He addressed the outburst on Twitter, in a string of tweets that have since been deleted.
"There's times when I get upset," he said.
"Times when I get angry, there's time's when I'm going to be frustrated. But I'm always going to be myself on stage."
Support for his BST shows comes from pop acts Tove Lo, Anne-Marie and Martin Garrix.
The 2017 BST festival has previously announced headline slots from Green Day, Kings of Leon and Phil Collins.
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Pop star Justin Bieber will bring his Purpose world tour to the BST festival in Hyde Park, it has been announced.