Lewandowski took his tally in the competition to 15 goals for the season, in what was just his ninth appearance of the campaign, after netting in Bayern's 3-0 Champions League semi-final win over Olympique Lyon on Wednesday.
In doing so, the Poland international secured Bayern's spot in the showpiece final, in which they will face Paris Saint-Germain on Sunday, and surpassed Messi's best-ever return in a single season in a competition.
Messi netted 14 times in 11 appearances during the 2011/12 edition, although that figure was bettered three times by Cristiano Ronaldo, who holds the competition's overall record with the 17 strikes he netted in Real Madrid's triumphant 2013/14 campaign.
Lewandowski will need to score twice in this weekend's final in order to match Ronaldo's record, although his main focus will be on winning his first Champions League crown, and Bayern's sixth overall.