FIFA, which is due to give its verdict later in the day on state of readiness, tried to wash its hands over the crush on Sunday at Makhulong stadium in a township near Johannesburg where Nigeria were playing North Korea.
"This friendly match has no relation whatsoever with the operational organisation of the 2010 FIFA World Cup, for which we remain fully confident," football's world governing body said in a statement.
But the headlines on the front-pages of South African newspapers made uncomfortable reading for organisers who have long had to fend off claims that South Africa's beleaguered security forces will struggle to keep order.
"Soccer Stampede Mayhem", read the headline in The Star which quoted one of those injured as having feared for her life.
"When we were coming in, they were just stepping on us," Princess Mbali said. "I thought I was dying. I was at the bottom."
Officials said one police officer was seriously injured and 15 people sustained minor injuries in the stampede at Tembisa township as a mass of supporters without tickets tried to force their way into the ground.
Speaking at the ground, police spokesman Lieutenant Colonel Eugene Opperman said that 8,000 free tickets had been distributed ahead of the match but other fans without tickets had tried to push their way in shortly before kick-off.
"There were supposed to be only 8,000 tickets -- they were all free," he told AFP.
Police said it was not immediately clear who had distributed the tickets and FIFA said that it was nothing to do with them.
"Contrary to some media reports, FIFA had nothing to do with the ticketing of this game," its statement said.
While a number of FIFA officials were present at the game, all refused to talk to the media and there was no customary post-match press conference.
Rich Mkhondo, a spokesman for the Local Organising Committee, also tried to brush off the episode and instead said the only concern remained over traffic jams.
"Our only concern is that people should park their cars at home and not clog up the streets around the stadiums," he told Talk Radio 702.
The episode served as a sharp reminder of the challenges facing the tournament which begins on Friday when the host nation plays Mexico and evoked ugly memories of previous crowd trouble in South Africa.
Forty-three people were killed in 2001 when ticketless fans tried to barge their way into the Soweto derby between the Orlando Pirates and Kaizer Chiefs which was being played at Ellis Park, a stadium in Johannesburg which is one of the 10 venues for the month-long tournament.
South African fans have traditionally arrived late for matches, with kick-offs often delayed to accommodate everyone.
But with delays ruled out at the World Cup, FIFA has been urging fans to get there on time.
The incident came just hours after South African President Jacob Zuma announced that everything was ready for the tournament -- the first World Cup to be played on African soil.
Makhulong, an all-terrace former first division ground which is not regularly used these days, is not one of the World Cup venues.
Police have drawn up a major security programme to cover all the matches which will include a closure of roads within a half-mile (800 meter) radius and a major deployment of officers.