The Polish international missed the 2-1 Group B win over Celtic in Glasgow that saw the German champions reach the knock-out stage of Europe's elite competition for the 10th successive season.
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Bayern coach Jupp Heynckes, undefeated in his fourth spell in charge of the German giants after replacing Carlo Ancelotti last month, was forced to field on-loan Real Madrid midfielder James Rodriguez up front with Thomas Mueller also missing out through injury.
However, the veteran tactician was confident Lewandowski would return to lead the line against Dortmund on Saturday as they travel to face their rivals, who are just three points behind them in the Bundesliga.
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"Obviously it's not my ideal choice to replace somebody up front with a midfield player but I had no choice," said Heynckes. "In my opinion the team did very well with the changes. But Lewandowski trained well today and seems fit. Hopefully all things being well he will play on Saturday."
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