Ballack has been suffering from a calf injury, but despite declaring himself fully fit for the Costa Rica game Klinsmann opted to keep him on the bench.
"The doctors said that he was at risk and that he might be forced to miss the whole World Cup if the injury got worse as the calf problem wasn’t fully over," Klinsmann was quoted as saying by SkySports.com.
Ballack said that despite his disappointment for not playing he accepts his coach's decision.
"I did everything to get fit and play but the coach decided otherwise, Jurgen and I had different opinions and he thought he had to hit the break and I accept his decision," Ballack said.
"This isn’t about individual players, but about the well-being of German football," the new Chelsea man added.
Klinsmann confirmed that he has no personal problems of any kind with his skipper but said that choosing the team will always be his own responsibility, adding that he's looking forward to play Ballack against Poland on Wednesday.
"I don’t have a problem if a player is keen to play any game, but the decision is mine at the end," Klinsmann said.