"After an exhaustive internal process, we now can acknowledge that there were inaccuracies in relation to Farhad and Junaid Dockrat in the article and we wish to set the record straight," it said in an apology posted on its website.
"We acknowledge that we are not in possession of evidence to show that Farhad Dockrat or Junaid Dockrat are linked to Al-Qaeda or any other terrorist organisation."
The website also had no evidence that Farhad was seeking seclusion on Greylock, or in Tsitsikamma, for the purposes of establishing terrorist training camps or that they were conducting any illegal activities.
It said its article suggested these links and that there was a strong Al-Qaeda presence in South Africa.
"We unequivocally and unconditionally apologise to Farhad and Junaid Dockrat and the Muslim community of South Africa and retract this allegation," the Daily Maverick said.
"We regret the inconvenience and distress it has caused to Farhad and Junaid Dockrat and the Dockrat family."
It said that in the interests of "good and ethical investigative journalism" it agreed to remove the article from their website.
The Daily Maverick reported in May that the police's crimes against the state unit and the State Security Agency (SSA) monitored training of al-Qaeda "terrorists" in South Africa without taking action.
"Operation Kanu" was reportedly launched to "investigate extremist Muslim activities" in South Africa, shortly after the 9/11 World Trade Centre attacks in the United States, and was crime intelligence driven.
The Daily Maverick said in its initial article "at the centre of this alleged terrorist network are several members of the well-known and influential Dockrat family".
It reported that Farhad and Junaid's names were forwarded to the United Nations' Security Council's Al-Qaeda and Taliban sanctions committee for designation, but that South Africa put an indefinite hold on the designation process.
According to the online publication, three months after they were put on a US "terrorist list" in 2007, the Dockrats moved their operation from Pretoria to the farm, Greylock, in the Klein Karoo.
There was a court dispute over a communal water line and the Dockrats later bought a 70% share of the developing Tsitsikamma Golf Estate.
Daily Maverick said in its apology that information that the United States Treasury listed the two on its list of persons associated with terrorism, and that they were placed on the US Sanctions list was correct.
"We wish to record that in 2007, South Africa objected to the proposal of the United States that Farhad and Junaid Dockrat be placed on the United Nations' Al-Qaeda Sanctions List," it said.
"However, we acknowledge that it is significant that they were not also placed on the UN list, and our article should have emphasised this more than just state that Farhad and Junaid Dockrat deny the US claims."
It said it was also wrong to say in its report that Farhad had lost a court case regarding water rights on his Greylock farm.
"Although some farmers in the area told us that the dispute was resolved in their favour, we accept that this was not the case and that the opposite was true."
Daily Maverick editor Branko Brkic said in a post on the website that he was "personally responsible for this failure" and that the online publication "stumbled" on the story.
"Going through an internal investigation and the realisation that one was wrong is an experience I don't particularly wish to repeat in this life," he said.
"But as humbling as this process is, it has reaffirmed to me what is most important - our readers, and the truth."
De Wet Potgieter, who wrote the report, said in a post that he was under pressure from some of his sources to publish his findings.
He acknowledged that he could have been "manipulated" by his sources.
"As an investigative journalist I have a duty to inform the public and believe the truth needs to be told," he said.
"I had no ulterior motives and am convinced that once the whole story has been understood, a clearer picture will emerge."
Source: Sapa, via I-Net Bridge
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