"This is because there was no violation of the Fifa disciplinary code."
South Africa were second best to a Diego Forlan-inspired Uruguay at Loftus Versfeld Stadium in Pretoria.
Atletico Madrid forward Forlan scored two and played a significant role in the third, scored deep into injury time by Alvaro Pereira.
It was the circumstances surrounding Forlan's second goal, scored from the penalty spot after Luis Suarez was fouled by Khune - an infringement which saw the goalkeeper shown a straight red card - that most angered Parreira, although he admitted that he himself was blocked from seeing the incident.
SA coach Parreira slams referee
He was also upset at the bookings handed out to midfield duo Steven Pienaar and Kagisho Dikgacoi, the latter of whom will now miss the final group game against France as a result.
"He was giving yellow cards that weren't yellow cards. He doesn't deserve to be here," said Parreira.
While feeling the result was harsh on his side, Parreira admitted that Uruguay had proved able opponents.
"The result doesn't reflect what happened in the match," the Brazilian added. "But Uruguay are a good team with good players, like Forlan. Their experience told at important moments."
While the result leaves Uruguay on four points going into their final game with Mexico and in pole position to qualify, South Africa prop up the group with one point heading into their clash with the French in Bloemfontein on 22 June.
"Our hopes are not over," added Parreira. "We need to beat France, but we will have to be more aggressive. Everything will be decided in the last game."
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