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Podolski, 29, started his first match of the tournament in the 1-0 win over the U.S. in Recife, Germany's final match in Group G, but was replaced by Miroslav Klose at half-time.
Germany coach Joachim Low told a news conference on Saturday that the Arsenal forward, who has scored 46 goals in 116 appearances for Germany since making his international debut 10 years ago, would not feature in Monday's clash in Porto Alegre.
"Podolski will be missing in the last 16," Low said, adding that the injury problem was not too serious.
"He's pulled a muscle. He needs two or three days of rest. If we reach the next round, there will be no problem," he explained.
Low added that defender Jerome Boateng, who has started all three of Germany's matches so far but was substituted at half-time in the 2-2 draw with Ghana, should be fit to fit to start against Algeria.
"He has a slight niggle in his knee," he said. "But that's no problem -- he will train with the team tomorrow."