Pienaar: First goal took wind out of sails
But the hosts also rounded on Swiss referee Massimo Busacca for a controversial second half penalty while Itumeleng Khune, sent off for a 76th minute tackle on Luis Suarez, apologised for conceding the spot-kick and his subsequent dismissal
"The first goal was crucial, it really caught us by surprise," said midfielder Steven Pienaar after the 3-0 defeat, "After that Uruguay are a well organised side at the back and we couldn't break them down."
"All the goals came from our mistakes," added winger Siphiwe Tshabalala, the man of the match in Friday's Group A opener against Mexico but largely ineffective on Wednesday.
"There are days when you try everything but things do not work out."
Midfielder Kagisho Dikgacoi, whose caution means he is out of the next match against France, said the penalty decision and red card for Khune had been harsh.
"I thought we were going to bounce back but then we got a penalty and a red card against us. The referee was not fair," he said.
Khune, who will also be out against France in Bloemfontein on Tuesday, said he had apologised to his teammates.
"It wasn't deliberate but I think I owe them an apology," he said. "I must apologise to the people too because they have been there for us and for something to happen like that, wasn't nice."
South Africa now face the real prospect of becoming the first World Cup hosts to fail to get past the first stage of their own tournament.