The dispute pitted pro-Europe billionaire Richard Branson, founder of Virgin, against the eurosceptic and right-leaning Daily Mail, after a memo sent to Virgin Trains staff that the newspaper was "not at all compatible" with the company's brand and would no longer be sold on its trains.
"Absurd ban on Daily Mail by Virgin! Pompous, censorious and wrong #virginontheridiculous," Johnson said in a tweet.
A spokeswoman for Virgin Trains said the firm decided to stop carrying the newspaper in November last year "after feedback from our people".
The memo to staff went further than that and said there was "considerable concern raised by colleagues about the Mail's editorial position on issues such as immigration, LGBT rights, and unemployment."
The Daily Mail, which is owned by Daily Mail and General Trust, said Virgin had initially told the paper it was dropping it to save space on its trains.
"It is disgraceful that ... Virgin Trains should now announce that for political reasons it is censoring the choice of newspapers it offers to passengers," the Daily Mail said in a statement, adding that the train company would only sell the Mirror, Financial Times and the Times.
"It may be no coincidence that all those titles, like Virgin owner Sir Richard Branson, are pro-Remain."
The Daily Mail has been at the centre of a number of spats over free speech, as campaign group "Stop Funding Hate" have lobbied companies to end their advertising in the newspaper.
In November, stationery retailer Paperchase apologised for a promotion in weekend editions of the newspaper after a backlash from campaigners.
Defenders of the Mail say the campaign against the newspaper infringes on freedom of the press.
A spokesman for Prime Minister Theresa May said that the decision to stock the Daily Mail was a matter for Virgin Trains but that press freedom was important.
"(May) has always been clear on the importance of a free press to our democracy and to our society," the spokesman said.
(Reporting by Alistair Smout; editing by Stephen Addison)
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)