The world and European champions suffered a surprise 1-0 reverse at Soccer City in Johannesburg, the scene of their 2010 FIFA World Cup final triumph over the Netherlands.
Bernard Parker scored the only goal of the game in the 56th minute, dinking over Spain goalkeeper Victor Valdes, who was forced off with a serious-looking right knee injury later in the match.
Del Bosque's men nearly mustered an equaliser, with Raul Albiol only denied by an outstanding Itumeleng Khune save late on, but South Africa held on for a famous win.
"It could be (our worst recent performance)," Del Bosque told Spanish television station Cuatro.
"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.
"They (South Africa) got better as the game went on (though)."
The loss was Spain's first since the 2013 FIFA Confederations Cup final, in which they were defeated 3-0 by hosts Brazil.
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