The split comes 15 months after a sex-and-drugs video featuring the former rugby player and a stripper was released.
After vehement denials, Van der Westhuizen, 38, finally admitted - in his biography, released late last year - that it was indeed him in the 29-minute video enjoying oral sex and sniffing white powder.
Delyse Vittone, Amor's mother and manager, confirmed yesterday that the two had separated.
"They just want to be left alone to sort out their differences," she told The Times.
Vittone and the couple's two children have allegedly moved in with a family friend.
The sex-tape scandal took its toll on the 37-year-old mother of two, who poured her heart out in a two-hour radio interview last year.
She wept as she spoke about how she felt betrayed by her husband's infidelity.
"I am not in a good space. The first time Joost told me the truth that it was him in the video was in August. [Until then] I had backed him .
"I just really feel I have been let down," she said.
Vittone said there had been rumours about her husband's cheating before the video became public.
Vittone admitted in the interview that their marriage was "strained".
"Honestly, I don't know if this will ever be OK [but] I am willing to give it 110%. I am trying to find the goodness out of it, something to learn out of it."
Vittone and Van der Westhuizen were married in a high-security and much-publicised wedding in December 2002.
Well they say that the "truth shall set you free" if you tell it that is, but Joost chose to lie and now the Chickens have come home to roost or is that Joost