The Poland international initially carried on following a heavy challenge from Porto defender David Carmo, but he was eventually substituted in the 34th minute of the match.
Lewandowski was seen with an ice pack around his leg when he took his place on the bench, and the La Liga champions have now revealed that the experienced forward damaged his ankle in the European match.
Barcelona have diagnosed him with "a left ankle sprain", and there are now fears that the 35-year-old could be set for a lengthy spell on the sidelines.
"Tests carried out this morning have revealed that Robert Lewandowski has a left ankle sprain. He is out and his recovery will determine his availability," read a statement on Barcelona's official website.
Lewandowski has been in impressive form for the Catalan outfit this season, scoring six goals and registering four assists in 10 appearances in all competitions.
Barcelona have not set a timeframe in terms of his recovery, but according to journalist Toni Juanmarti, the forward is likely to be out of action for at least a month.
Lewandowski is therefore set to miss his side's next four games in all competitions, which includes the home league fixture against Real Madrid on October 28.
The forward is also set to be absent against Granada and Athletic Bilbao in La Liga, in addition to the Champions League clash with Shakhtar Donetsk on October 25.
Lewandowski is one of four Barcelona players currently on the sidelines through injury, with Pedri (thigh), Frenkie de Jong (ankle) and Raphinha (hamstring) also out of action.
The forward made the move to Camp Nou from Bayern Munich in the summer of 2022, and he has scored 39 goals and registered 12 assists in 56 appearances for the Catalan outfit.
Lewandowski has another three years left to run on his deal, but there has recently been speculation surrounding his future with the La Liga champions.
A number of Saudi Arabian clubs are believed to be keen on the forward, with Abha said to be one of those keeping a close eye on his situation at Camp Nou.