De Villiers said he had made his previous comments "based on what I know of Schalk Burger as a player, and not on what occurred".
South Africa will not appeal against Burger's eight-week ban.
The world champions also saw second row Bakkies Botha handed a two-week ban for dangerous charging.
They have yet to decide whether to appeal against Botha's ban, and as a result have delayed naming their team for the third Test until Thursday - the same day as the Lions.
On Sunday Burger was found guilty of "making contact with the face in the eye area" of Lions wing Luke Fitzgerald.
Television footage showed Burger's fingers making contact with Fitzgerald's eye inside the first minute of the game in Pretoria.
Fitzgerald was able to continue after treatment, but at the time Burger escaped with only a yellow card from French referee Christophe Berdos, a decision taken on the advice of New Zealand touch judge Bryce Lawrence, who spotted the offence.
If the bans aren't working they have got to be longer
Former England hooker Brian Moore
Even after Burger was suspended De Villers continued to defend the 26-year-old, insisting: "I have watched the television footage, and am still convinced that nothing he did was on purpose. He is an honourable man - he never meant to go to anyone's eye."
But after a meeting with the South African Rugby Union (Saru) he finally apologised, along with South African rugby chief Oregan Hoskins.
"We would like to apologise to the rugby community for the erroneous impression that acts of foul play are in any way condoned by South African rugby," said Saru president Hoskins.
"That has never been the case, and is not now, and we support strong actions by rugby authorities when such acts occur."
The International Rugby Board (IRB) says it is looking into the issue of eye-gouging after the incident involving Burger and another involving Italy captain Sergio Parisse, who was also banned for eight weeks for a similar offence during Saturday's 27-6 defeat by New Zealand in Christchurch.
The IRB is awaiting the report from South Africa via their judicial officer Alan Hudson.
"The IRB does not condone any violent behaviour and there is no place for illegal play in our game," said an IRB spokesman.
Gouging yellow baffles Woodward
According to the IRB regulations, the recommended minimum sanction for "contact with the eye or eye area" is 12 weeks.
Meanwhile, former England hooker Brian Moore wants gouging bans to be increased.
"It's been a publicised issue, bans have been handed out but people aren't stopping doing it and if the bans aren't working they have got to be longer," Moore told the BBC.
"Rugby is a contact sport and you have to accept the risks but Burger gouged him, it was as simple as that. It can't be accidental and there is no place for it in the game.
"I don't know how Bryce Lawrence, who was the referee in the first Test and had the best view of this incident of anyone in the world, could not understand that there is no other sanction other than a red card for gouging.
"He is an elite referee and to get that wrong is scandalous."
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