The prolific Poland striker is facing up to the prospect of a month on the sidelines after damaging knee ligaments in his country's 3-0 win over Andorra.
It is a cruel blow for Lewandowski, who has 35 goals in the Bundesliga and looked well on course to at least match Gerd Muller's famous record of 40 in a single campaign, set back in 1971-72.
The 32-year-old is unavailable for this weekend's crunch clash with second-place RB Leipzig and will miss both legs of the Champions League quarter-final with Paris Saint-Germain.
For Flick, though, dealing with adversity is par for the course.
"These are situations that you have as a coach. I'm sorry for the player who got injured. I would like to have everyone with me," he told a pre-match news conference.