The singer departed the group's On The Road Again world tour last week after being signed off for stress, but has now made the decision to leave the band permanently.
"My life with One Direction has been more than I could ever have imagined," Malik said in a statement.
"But, after five years, I feel like it is now the right time for me to leave the band. I'd like to apologise to the fans if I've let anyone down, but I have to do what feels right."
In a joint statement, the remaining members of One Direction said: "We're really sad to see Zayn go, but we totally respect his decision and send him all our love for the future.
"The past five years have been beyond amazing, we've gone through so much together, so we will always be friends. The four of us will now continue.
"We're looking forward to recording the new album and seeing all the fans on the next stage of the world tour."
One Direction's label boss Simon Cowell added: "I would like to say thank you to Zayn for everything he has done for One Direction.
"Since I first met Zayn in 2010, I have grown very, very fond - and immensely proud - of him. I have seen him grow in confidence and I am truly sorry to see him leave.
"As for One Direction, fans can rest assured that Niall, Liam, Harry and Louis are hugely excited about the future of the band."
One Direction will continue their On The Road Again world tour in Jakarta, Indonesia tonight (March 25), before travelling to South Africa this weekend.
03-25-2015, 03:25 PM
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