ITV released a statement on Tuesday afternoon saying: “Following discussions with ITV Piers Morgan has decided now is the time to leave Good Morning Britain.
"ITV has accepted his decision and has nothing further to add.”
The news comes as TV watchdog Ofcom launched an investigation into comments made by Morgan on GMB about the Duke and Duchess of Sussexes' interview with Winfrey after it received more than 41,000 complaints.
During Monday’s episode, the presenter made dismissive remarks about Meghan's claims to have had issues with her mental health during the show.
An Ofcom spokesman said: "We have launched an investigation into Monday's episode of Good Morning Britain under our harm and offence rules.
"As of 2pm on Tuesday, 9 March, we have received 41,015 complaints about the programme.”
During Tuesday’s episode of GMB, Morgan stormed off set following a discussion about Meghan with his colleague Alex Beresford.
Weather presenter Beresford defended the couple, who have made global headlines following their bombshell interview with Winfrey.
He took Morgan to task, saying: "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…”
Edinburgh Council leader Adam McVey took to social media and branded Morgan as a “bully” after the TV presenter stormed off the set.
Mental health charity Mind were also quick to complain about Morgan’s comments on Monday.
The organisation previously said in a tweet it was "disappointed and concerned" by Morgan's comments and that “it's vital that, when people reach out for support or share their experiences of ill mental health, they are treated with dignity, respect and empathy."
ITV's chief executive Dame Carolyn McCall said on Tuesday the row was not "manufactured".
She added that ITV managing director of media and entertainment Kevin Lygo had been in discussion with Morgan in recent days regarding his coverage of the Harry and Meghan interview.
She said GMB was a "balanced show", adding: "ITV has many voices and we try and represent many voices every day. It's not about one opinion."
According to STV's data, audience figures for Winfrey’s Harry and Meghan interview peaked at 1.1 million during the programme and across the broadcast with an average audience of 984,000 viewers.
STV said that in terms of audience share, Oprah with Meghan and Harry attracted more interest in Scotland than elsewhere in the UK, with 58 per cent of TV viewers in Scotland watching it.
The broadcaster said: "STV's audience peaked at 1.1 million during the programme, and the interview has so far reached a total of 1.3 million viewers.
"That figure is expected to rise once ratings are consolidated in seven days, capturing catch-up data including viewing from STV Player."
Across the UK the interview peaked at 12.4 million viewers, and reached an estimated 17.1 million American viewers when it was shown on CBS on Sunday.