The announcement comes just five days after the 22-year-old dropped out of band's world tour citing "stress."
"My life with One Direction has been more than I could ever have imagined," Malik said in a statement published on the band's Facebook page.
"I am leaving because I want to be a normal 22-year-old who is able to relax and have some private time out of the spotlight."
Malik was forced to defend himself on social media recently amid rumours he cheated on his fiancée, Perrie Edwards of the band Little Mix, after he was photographed with another woman.
"I'm 22 years old ... I love a girl named Perrie Edwards," he tweeted at the time.
Before his departure authorities in the Philippines imposed a $5,000 "weed bond" on Malik and fellow band member Louis Tomlinson, with the money to be forfeited if either was caught using or promoting illegal drugs.
A video that circulated online last year appeared to show Malik and Tomlinson smoking cannabis and joking about drug use.
One Direction moves on.
The band released a statement expressing their sadness over Malik's departure.
One Direction's remaining members – Harry Styles, Niall Horan, Liam Payne and Louis Tomlinson – said they respected Malik's decision, and affirmed that they would "always be friends."
"The four of us will now continue," the statement reads. "We're looking forward to recording the new album and seeing all the fans on the next stage of the world tour."
The next scheduled date on One Direction's "One the Road Again" tour is in Johannesburg, South Africa, on Saturday.
The X-Factor creator Simon Cowell discovered One Direction in 2010 when the five members auditioned for the popular reality TV singing contest separately.
Since then, the band has gone on to international stardom, with 94 number No. 1 hits and over 46 million records sold. Forbes pegs the band's earnings last year at an estimated $75 million US.
Canadian fans can catch One Direction when the band plays a number of dates in the country in as part of its On The Road Tour in late summer and fall.