Bayern will travel to the Santiago Bernabeu needing to overturn a 2-1 deficit on Tuesday after Cristiano Ronaldo's double sunk Carlo Ancelotti's men on home turf last week.
But the Poland striker will be back to lead the line for Bayern in midweek as they seek to end Madrid's bid to become the first club to retain the title.
"I'm fine. I'm very pleased I was able to take part in training today. Everything's okay," Lewandowski told Bayern's official website.
Lewandowski has scored 26 league goals in the 2016-17 campaign, while he's managed seven in eight appearances in the Champions League.