The debate cannot legally go ahead without his inclusion.
MediaWorks confirmed that rather than scrap tomorrow's debate, they would include Mr Craig.
"We'll have to somehow squeeze him in," said director of news Mark Jennings.
But The Nation's Tim Watkin said the production values of the show would suffer as a result.
Each political leader will get less than five minutes to speak because of the late inclusion, he said.
"We don't agree with the judge's decision but we accept it," Mr Jennings said.
Earlier TV3 said Mr Craig's party did not meet the criteria to take part in the debate.
A spokeswoman said tomorrow's leaders debate focused on parties which had been represented in Parliament in the last three years.
Mr Craig's lawyer John McKay called that "a cop out" and in an affidavit Mr Craig described the decision as "arbitrary and unreasonable".
Conservatives won 2.6 per cent of the party vote in the 2011 general election - more than Maori, Mana, United Future or Act - but did not gain a seat.
Justice Gilbert said MediaWorks had acted unreasonably.
"The Conservatives are polling higher than four of the invited parties and one doesn't have a sitting MP," he said.
"It's characterised as a minor-party debate," said Mr McKay.
"It's just extraordinary Mr Craig isn't there. They've got pretty much everybody else."
MediaWorks submitted its in-house studio had room only for six political leaders and if they took it to a different studio it would cost an extra $40,000 to produce the show.
Mr McKay was sceptical as to whether that was a factor.
"It's extraordinary that they're the issues . . . is it really down to lecterns and lighting?"
In court MediaWorks' lawyer Daniel McLellan QC argued the media should not have it dictated to them what was newsworthy.
He said the debate was just one of a series and Mr Craig had been invited to other events closer to September.
"This debate is not likely to have a significant impact on the 2014 general election," said Mr McLellan.
Mr Craig had appeared on The Nation as many times as both the Prime Minister and leader of the opposition and Mr McLellan said it was certainly not a case of him being unfairly shunned.
"It's a highly competitive environment for politicians . . . but balanced against that is the media's right to determine the content," he said.