"South Africa were no better than us but we don't have enough quality to compete with the top teams although we deserved our place here."
Katanec said the loss of Sebastjan Cimirotic and Aleksander Knavs during the game because of injury hurt his side.
It is not clear yet whether the pair will miss the final Group B game against Paraguay.
Katanec, who takes charge of Slovenia for the final time against Paraguay, is hoping his side will be competitive in their final game.
"We showed we are competitive - we were in the game against Spain until the last five minutes and we played good football today.
"We will go into the last match with the same attitude as we want to
win a game in our first World Cup."
Slovenia keeper Marko Simeunovic said his team-mates never found their rhythm.
"We fulfilled our dreams by qualifying for the World Cup. Now we have to sit down and analyse our mistakes and do better against Paraguay."