MacKenzie, who used to edit the tabloid, wrote in July that Fatima Manji hosting the show was “massively provocative” following the Nice terror attack, which he called “yet another shocking slaughter by a Muslim”.
Manji called MacKenzie’s words “ill-informed, racist and Islamophobic” and was among 1,900 people to complain to the press regulator Ipso.
Ipso rejected the complaint on Wednesday, saying MacKenzie’s comment that Islam “was clearly a violent religion” was his opinion and therefore could not be deemed inaccurate.
It also held the article did not breach the clause on discrimination as it “did not include a prejudicial or pejorative reference to the complainant on the grounds of her religion”.
Ben De Pear, who edits the programme, said he was “dismayed” by the ruling.
He said: “Whilst we agree that freedom of expression is a fundamental right, we do not believe that it should be used as a licence to incite or discriminate.
“His inflammatory comments on Fatima Manji’s professional status, which were widely condemned, and his attempts to equate the wearing of a hijab with support for terrorism, have no place in a properly informed and tolerant society.”
De Pear continued: “We employ reporters based on their journalistic skills, not their ethnicity.
“We see no reason why a Muslim journalist should be prevented from covering any story and Fatima will continue to report and present the news on the issues of the day with impartiality and depth.
“We are grateful for all the support shown to Fatima during this difficult time.”
Ipso chief executive Matt Tee said: “We know our ruling will not please everyone but we are confident that our conclusion is the right one.”
He added: “Our Complaints Committee acknowledged in its ruling that many of those complainants, including Ms. Manji herself, found the article both distressing and offensive.
“In reaching its decision that the article did not breach the Code, the Complaints Committee noted the balance between protecting the rights of individuals with freedom of expression.
“While the code prohibits prejudicial or pejorative references to an individual, this is not the case for a particular religion, even though such criticisms may cause offence.
“IPSO is committed to a trusted, free and responsible press and will reach our judgements only after careful and considered discussion of the evidence we receive from complainant and newspaper.”
In an article for the Liverpool Echo in July, Manji referenced an infamous headline about the Hillsborough disaster the Sun ran under MacKenzie’s editorship.
“THE TRUTH?” she wrote. “I confess. I pi**ed on Kelvin MacKenzie’s apparent ambitions to force anyone who looks a little different off our screens, and I’ll keep doing it.”
She also referred to another Sun column by Katie Hopkins that was also subject to a huge number of complaints.
She continued: “The Sun, you will recall, is the newspaper that appears at ease with its columnists describing refugees dying at sea as “cockroaches”.
Manji continued: “But it’s dangerous to regard Mr MacKenzie and those who echo his Islamophobic sentiments as mere pantomime villains.
“Their soapbox allows them to spread their ill-informed, irresponsible and malevolent invective to millions of readers. Racist and Islamophobic rhetoric has real consequences – lives have been lost and shattered in our own country.”
Manji has not commented personally on the Ipso ruling.
The Sun declined to comment.