Lewandowski was present as Poland launched their new strip at the National Stadium on Tuesday afternoon but he will be back in Germany when Scotland face their Euro 2016 rivals on Wednesday night after failing to overcome a knee strain.
Poland were already without their captain, Lewandowski's Dortmund team-mate, Jakub Blaszczykowski, who suffered cruciate ligament damage earlier this year.
Another Dortmund player, defender Lukasz Piszczek, will captain the team instead.
Head coach Adam Nawalka said: "They are important players in our plans but life goes on and their absence provides an opportunity for other players."
The coach hinted that Arsenal goalkeeper Wojciech Szczesny would start ahead of Southampton's Artur Boruc, who played under Scotland manager Gordon Strachan for Celtic.
Nawalka played down the importance of playing against one of their group rivals in the European Championship qualifiers, although he is looking for improvement on their most recent home games.
The Poles suffered a 2-0 defeat by Slovakia and a goalless draw with the Republic of Ireland, although they beat Norway and Moldova during a Middle East training camp in January.
He said: "It doesn't matter that Scotland are our rivals in our qualification group because the decision was made months ago.
"They have a good level of skills and they will show a lot of fight on the pitch.
"It's an important game in preparation for the European Championship. I hope our organisation is at a higher level than previous matches against Slovakia and Ireland."