The Channel 4 debate, which was scheduled for Sunday, would have been the second direct clash between Mr Johnson and the Labour leader after a contest on ITV this week.
But despite agreement from Labour, a producer announced on Thursday evening that the programme had been cancelled just days before it was supposed to air.
"Gutted we’ve had to cancel a planned Leaders debate on Channel 4 for this Sunday. Jeremy Corbyn had agreed to take part but, after many weeks of intense discussion, we were unable to secure agreement from Boris Johnson team," said Channel 4 producer Louisa Compton.
Channel 4 News anchor Krishnan Guru-Murthy, who would have presented the debate, added: "Boris Johnson said he was in favour of debates and his team have been in detailed talks with us for weeks about format and rules right up until yesterday.
"They insisted they were engaged and wanted to take on Jeremy Corbyn on our channel. Corbyn said yes. Offer still stands."
It comes as the Labour candidate in Mr Johnsons's seat said the prime minister was ducking out of a local hustings event there, leading it to be cancelled as well.
Ali Milani tweeted: "Name any time that works for you. My team will organise the venue, details and all logistics. All you have to do is show up. Show an ounce of integrity. Come debate me. What do you have to worry about?"
Channel 4 says it will still hold a live debate on 8 December featuring "representatives" of seven major parties taking questions from an audience of undecided voters. The politicians would be questions about everything except Brexit.
Another head-to-head clash is expected to take place on the BBC on Friday 6 of December, with Question Time specials planned for this Friday and further events potentially in the pipeline.
The ITV debate on Tuesday was the first ever head-to-head television clash between the two leaders of the main parties. The first televised debates took place in 2010 and were a three-way contest, while David Cameron and Theresa May both avoided head-to-head debates in 2015 and 2017, instead preferring other formats.
Pollster YouGov found Boris Johnson and Jeremy Corbyn were roughly neck-and-neck in the contest, with 51 per cent of the audience saying the Tory leader won and 49 per cent saying the Labour leader. But among undecided voters Mr Corbyn was judged to have won a decisive victory, with a 59-41 per cent lead over Boris Johnson as best performer among that group.