The Scottish comedian made the comment about the current Prime Minister on Channel 4 satirical show The Last Leg, comparing him to The Terminator and wishing he would be "dragged screaming into hell".
The gag prompted 11 complaints to the TV regulator, which Ofcom said “did not raise issues warranting investigation”.
Boyle, 49, was reacting to Johnson ending his final Prime Minister’s Questions in July - after stepping down as leader - with the words: “Hasta la vista, baby.”
Boyle said: “You finished with a quote from The Terminator. The Terminator because you killed 150,000 f***ing people during the pandemic.
"I don’t want to sound like I’ve got a grudge or anything, but I hope a vent opens up in the ground and clawed hands drag you screaming into hell."
Watch: Frankie Boyle's Boris Johnson Terminator joke
The Glasgow stand-up comic is known for his controversial jokes, which aim to cause offence.
In 2008 he was criticised for making fun of Olympic swimmer Rebecca Adlington’s appearance.
In 2010 Mencap called him out on jokes about people with Down syndrome.
Boyle recently dismissed comedians who claim to have been "silenced" due to cancel culture.
He said: "I'm not one of those comedians who's like 'ooh, I've been silenced'. I hate those people.
"Any time I hear someone saying that, I always think: 'How come I can still hear you?'"
But he told Backstage with Katherine Ryan that he has "become terrified of social media" and now often refrains from tweeting edgy jokes.
Boyle added: "Sean Connery died and it was like quite early in the morning when the news came in so I was one of the first people to see the news.
"I thought of tweeting: 'They've shaken him and he's not stirred'. Then I just thought 'no, I cannot'."