The story claimed that al-Qaeda was alive and well in South Africa and implicated cousins Farhad and Junaid Dockrat in setting up military training camps for the terrorist group in the country.
The story was picked up by several local news organisations but in the days after it was published, there was widespread outcry over the lack of apparent evidence to prove these claims.
On Tuesday the fact-checking website Africa Fact Check published a point-by-point analysis, originally written by the community journalism project GroundUp, which said that the story presented no convincing evidence.
At the time De Wet Potgieter, the reporter who wrote the story, told the Mail & Guardian and other news sites that further evidence would be forthcoming in a subsequent story.
But on Wednesday the Daily Maverick issued an apology to the Dockrats and retracted the story. The story is no longer available on the Daily Maverick 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, or that Farhad Dockrat was seeking seclusion on Greylock, or in Tsitsikama, for the purposes of establishing terrorist training camps or that Farhad Dockrat and Junaid Dockrat were conducting any illegal activities," it said.
"Our article suggested these links and also that there is 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. We regret the inconvenience and distress it has caused to Farhad and Junaid Dockrat and the Dockrat family."
In an editorial published on the site, editor Branko Brkic took personal responsibility for publishing the story, saying the organisation had "stumbled on this one".
"While we are not unique in this, it hurts desperately that we have published a story that ultimately should not pass our own final test – that every single story, as written, was fully, rigorously and critically examined and that, ultimately, was complete in every detail," he wrote.
Potgieter also published a comment piece in the Daily Maverick on Thursday explaining how he had come to write the story.
"During the research for this story, I have been immersed in claims and counter-claims and believed I had managed to successfully extricate the truths from the disinformation. I was under immense pressure from some of my sources to publish my findings, being led to believe that this would force the hand of the authorities to act on the evidence the operatives said they had provided. These undercover operatives would then be in a stronger position to provide me with more direct evidence," he wrote.
According to Potgieter, a promised second wave of evidence failed to materialise.
"I was caught up in the twilight realm of a power play in the intelligence world, and I have paid the price," he said.