Video report from ITV News Arts Editor Nina Nannar
The announcement comes after broadcasting regulator Ofcom launched an investigation after it received more than 41,000 complaints regarding comment made by the presenter following Harry and Meghan's interview with Oprah Winfrey.
In a statement, the broadcaster said: "Following discussions with ITV, Piers Morgan has decided now is the time to leave Good Morning Britain.
"ITV has accepted this decision and has nothing further to add."
The Duchess of Sussex opened up about her suicidal thoughts during her time in the Royal Family in a deeply personal and explosive interview with Oprah Winfrey. Meghan said she got to the stage where she “just didn’t want to be alive anymore.”
After the clip aired, Morgan said during Monday’s programme: “I’m sorry, I don’t believe a word she says.
Piers Morgan storms off Good Morning Britain following heated discussion with co-presenter Alex Beresford
“I wouldn’t believe her if she read me a weather report.”
An Ofcom spokesperson said: “We have launched an investigation into Monday’s episode of Good Morning Britain under our harm and offence rules.”
During Tuesday’s programme, Morgan addressed his comments about Meghan’s mental health.
He said: “When we talked about this yesterday, I said as an all-encompassing thing I don’t believe what Meghan Markle is saying generally in this interview, and I still have serious concerns about the veracity of a lot of what she said.
“But let me just state on the record my position about mental illness and on suicide. These are clearly extremely serious things that should be taken extremely seriously, and if someone is feeling that way they should get the treatment and help they need every time."
Morgan also stormed off set on Tuesday after co-presenter Alex Beresford branded his behaviour "diabolical" following his controversial remarks.
Speaking about the death of Diana, the 55-year-old former newspaper editor said Harry "couldn't let it go", but "William went through the same thing and he's managed to come to terms with the media and he works with the media".
Weather presenter Beresford then interjected and said the Royal couple had "had an overwhelming amount of negative press".
"There was bad press around the engagement... and everything that has followed since."
He added this had "been incredibly damaging, quite clearly, to Meghan’s mental health and also to Harry...
“And I hear Piers say William has gone through the same thing but, do you know what, siblings experience tragedy in their life and one will be absolutely fine and brush it off and the other will not be able to deal with it so strongly and that is clearly what has happened with Harry in this situation.
Meghan tells Oprah about “concerns and conversations' about Archie's skin colour
“He walked behind his mother’s coffin at a tender, tender age in front of the globe. That is going to shape a young boy for the rest of his life, so I think we all need to take a step back, and I understand that you don’t like Meghan Markle, you’ve made it so clear a number of times on this programme…”
“And I understand you’ve got a personal relationship with Meghan Markle or had one and she cut you off.
"She’s entitled to cut you off if she wants to. Has she said anything about you since she cut you off?
"I don’t think she has but yet you continue to trash her…”
Morgan then stood up and said: “OK, I’m done with this” and walked off set, saying: “Sorry, no… sorry, can’t do this…” as he stormed off set as Beresford called his actions "diabolical behaviour".
Hours after the announcement of his departure from the breakfast-time programme, Morgan shared a tweet in homage to the late John Ferriter, his former manager and friend.
It read: "Thinking of my late, great manager John Ferriter tonight. He’d have told me to do exactly the same thing. #TrustYourGut"
Oprah With Meghan and Harry is available to watch on demand on ITV Hub for viewers in the UK.