Klose, who came down with the virus after Germany's semi-final defeat by Spain on Wednesday, was a goal away from equalling Brazilian Ronaldo's record of 15 goals and at 32 years old is unlikely to play in the next World Cup.
Low said clinching third place was Germany's priority and Klose's inclusion could have damaged his side against Uruguay in the third-place play-off, a scintillating match his team won 3-2 after trailing 2-1 at one stage.
"We needed 100 percent from everyone so we couldn't afford to use players who are not fit," Low said after the win, which capped an impressive tournament for a young and inexperienced team largely written off in the run-up to South Africa.
"This is why we didn't field injured or ill players. It would have been irresponsible. He simply couldn't play, he failed the fitness test," he added.
Klose recently finished one of the worst seasons of his career for Bayern Munich but was one of Germany's best-performing players in the tournament, scoring four of their 13 goals and putting himself in contention for the Golden Boot award.
DEVASTATED KLOSE
Low said he empathised with Klose, who was bitterly disappointed but had admitted himself that playing in the last match would have been a mistake.
"He wanted to play but he said there was no point because he could only play a few minutes," Low said. "He could hardly walk. There was no way I could have played him.
"Just imagine his feeling. You want to get a record. He really wanted to play and was absolutely devastated but he knew it was the team that was important."
Attacking midfielder Thomas Muller and Uruguayan striker Diego Forlan netted in the play-off to draw level in the scoring charts with five goals alongside Spain's David Villa and Dutchman Wesley Sneijder, who are certain to play in Sunday's final.
Muller's absence through suspension for the semi-final defeat was seen as a major factor in Germany's below-par performance against the Spanish but he insisted his team had proved their worth and could hold their heads up high.
"I couldn't play in the semi-final so it was important to put on a great show and luckily I could contribute to our victory," Muller said.
"We've shown we can perform at the top level. We've concluded in a very satisfactory way and the German people can be proud."
