The broadcast in March was the most complained-about TV episode of 2021, prompting 54,595 complaints to the media watchdog.
Morgan said he did not believe Meghan's claims about her mental health, made during her headline-grabbing interview with Oprah Winfrey. After clashing with a co-presenter, Morgan departed the programme for good.
Responding to the announcement on Twitter, he said: "Delighted to have perpetrated the most complained about moment on UK TV for 2021 ... especially because every single one of the absurd complaints was rejected."
Adam Baxter, Ofcom's director of standards and audience protection, said: "Interestingly, it's a relatively small number of TV shows driving the lion's share; the top five most-complained about programmes account for 80 per cent of all complaints.
"Social media - a digital home for modern-day water-cooler conversations - also has its influence on complaints figures.
"But for me, these volumes demonstrate the British public's interest and passion for TV and radio programmes, and shows just how important they are to the cultural fabric of our nation."
ITV's Love Island was in second place thanks to an August episode, in which contestant Faye Winter delivered a lengthy expletive-laden outburst towards her partner Teddy Soares, prompting 24,921 complaints.
The pair had an explosive argument after the islanders were played a clip of Soares telling another contestant, Clarisse Juliette, who had since been eliminated, that he was attracted to her.
In third place was Celebrities: What Happened To Your Face on Channel 5, which looked at plastic surgery in celebrity culture, with 7,125 complaints made about remarks made about the appearance of a number of stars featured in the programme.
Harry and Meghan's bombshell interview with Winfrey, which broadcast on ITV in March, was the fourth most complained-about show of the year, with a total of 6,486 complaints.
In that programme the Sussexes first accused the royal family of not supporting them, claimed royal aides declined to help Meghan when she was troubled with suicidal thoughts and said a relative had made a racist comment about their son's skin colour.
Love Island also delivered the fifth most complained-about episode of the year.
The arrival of a postcard from rival villa Casa Amor to the main villa on the ITV show prompted 4,337 complaints to Ofcom.
The postcard showed the male contestants on the show in compromising circumstances with a new group of girls, despite many already being coupled up.
Mr Baxter said the high number of complaints do not necessarily mean rules have been broken.
He said: "The judgments we make each day are often finely balanced - such as our highest profile case this year: Piers Morgan's comments on Good Morning Britain in the wake of the Duke and Duchess of Sussex's interview with Oprah Winfrey.
"But, given the importance of the right to freedom of expression, we only step in or take action against a broadcaster when we consider it necessary."
Ofcom this year concluded 33 investigations and recorded 20 breaches, with many of these about hate speech or coronavirus misinformation.
BBC figures were not included in the tally but the corporation's coverage of the death of the Duke of Edinburgh in April drew 110,000 complaints within a week – the highest number ever published in the UK about television programming.
The most complained-about programmes of 2021:
1. Morgan's comments about Meghan's mental health on Good Morning Britain (54,595)
2. Faye Winter's expletive-laden outburst towards Teddy Soares on Love Island (24,921)
3. Oprah Winfrey's interview with Harry and Meghan (6,486)
4. Remarks about famous figures on Celebrities: What Happened To Your Face (7,125)
5. The postcard from Casa Amor on Love Island (4,337)
6. A discussion about the number of unvaccinated people in hospital on Lorraine (3,769)
7. Discussion between Morgan and Alex Beresford on Good Morning Britain (3,249)
8. Dr Hilary Jones criticises a fake Covid-19 information pamphlet on Good Morning Britain (2,632)
9. A Good Morning Britain segment titled: "Ditching unvaccinated friends?" (2,104)
10. A This Morning segment called: "How to lose the lockdown pounds" (1,942)