The world and European champions made seven substitutions - one more than is permitted in international friendlies by soccer's ruling body.
Match officials allowed Pepe Reina to come on for injured goalkeeper Victor Valdes after Spain had already made six changes, much to the chagrin of South Africa coach Gordon Igesund whose protests were waved away.
Spain, who used Iker Casillas in goal in the first half, brought Valdes on for the second period but the Barcelona keeper twisted his knee in the 78th minute and had to go off.
Bernard Parker had chipped the ball over Valdes for the only goal after 56 minutes for South Africa who missed out on qualifying for the 2014 World Cup in Brazil.
Goalkeeper Itumeleng Khune had to make a flying save in the final minute to deny Raul Albiol an equaliser.
Asked by Spanish television broadcaster Cuatro if it was Spain's worst performance in recent times, coach Vicente Del Bosque replied: "It could be. I think we can even say the defeat was well deserved.
"We started well but little by little they started to open us up and we allowed them time to counter attack.
"We came out with good intentions and fought to the end to find an equaliser so I can't complain about the players' attitude," added Del Bosque.
"They (South Africa) got better as the game went on."
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A crowd of around 40,000, less than half the capacity, watched the World Cup trophy being paraded by the Spanish players before kickoff while midfielder Xabi Alonso addressed the crowd to thank them for their support three and a half years ago.
Spain had the ball in the net inside five minutes but the goal was ruled out for offside.
South Africa nearly took the lead in the 18th minute when Oupa Manyisa's long-range effort took a deflection off Sergio Ramos and dipped over Casillas, hitting the crossbar before bouncing away.
Casillas then came to Spain's rescue as he palmed away a shot from Parker.
"It was a fantastic result and you can't take the win away from us," Igesund said.
The only goal came after a swift counter-attack started and finished by Parker.
"A goal against the World Cup winners is a career highlight for me," said Parker.
(Reporting by Mark Gleeson, editing by Tony Jimenez)
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