The team, who are due to play five One-dayers in Zimbabwe, are spending the night here as talks continued over resolving the latest crisis which was sparked when the Harare authorities imposed a ban on a large section of the travelling British media.
In total, eight British reporters were refused accreditation for the series which is due to get underway on Friday.
Leading players are understood to be unhappy about the media ban which could prompt the tour to be called off.
However, the England and Wales Cricket Board (ECB) could be hit with huge fines and even suspension if they fail to honour their commitment to the tour.
"The England and Wales Cricket Board (ECB) chairman David Morgan has instructed the team to stay put for the night in Johannesburg," said Richard Bevan, Professional Cricketers Association chief.
"He is currently in Harare in discussions with authorities there," said Bevan, adding he could not give any indication whether England would board a plane for the Zimbabwean capital on Thursday.
Public broadcaster SABC radio reported that the decision to offload baggage from the planned flight from Johannesburg International Airport was taken at around 6.00 pm (1600 GMT).
Andy Walpole, ECB spokesman told Sky News: "(Morgan) asked us to cancel the team's flight and spend the night at the airport so talks could continue between ECB and Zimbabwe Cricket Union (ZCU) to get the ban overturned."
"It is an evolving situation. We're continuing to talk to the ZCU, the embassy in Harare and players' representatives."
Meanwhile, the Foreign Office in London summoned Zimbabwe's charge d'affaires to express "deep concern" at the refusal of visas to the British journalists.
The International Cricket Council (ICC) said that it is continuing to monitor developments.
ICC president Ehsan Mani said that given the confusion over the accreditation of several English journalists it was an understandable decision for the ECB to instruct its players to remain in South Africa.
"The ICC understands the decision of the ECB to allow its players to remain in South Africa overnight," said Mani.
"There are serious concerns about the issue of media accreditation but until further information is available it is difficult to effectively address the issue.
"As well as urgently seeking a solution from within Zimbabwe, I am in the process of speaking to the other directors of the ICC to determine their views on this issue."
The England squad and the travelling media, who arrived here from Windhoek, had been due to touch down on Wednesday night in Harare for the start of the 10-day tour which has been widely condemned because of the land reform policies of president Robert Mugabe.
But on Tuesday, the Zimbabwe government released a list of journalists who would be banned from making the trip which included reporters from BBC radio and television, Daily and Sunday Telegraph, Times and Sunday Times, The Sun, Daily Mirror and News of the World.
That prompted calls for the tour to be called off but Mani said the ICC, who had highlighted to the England and Wales Cricket Board the possible financial implications of a boycott, would endeavour to seek a resolution to the situation.
Mani refused to accept that in the light of the media ban and the obvious political intervention by Mugabe's regime it now fell upon the ICC to call off the tour.
"That is not a matter for me to decide at this stage," he said.
"I believe the two matters (the tour and Zimbabwe's politics) are totally unrelated. We accept that cricket and politics do mingle but our responsibility is to cricket and it is for politicians to deal with politics.
"Two wrongs don't make a right."