The accolade went to Borussia Dortmund's Pierre-Emerick Aubameyang, who struck twice in a 4-3 win over Werder Bremen on the last day of the campaign to take his tally to 31.
That was one more than Lewandowski, who drew a blank in a 4-1 home victory over Freiburg.
The 28-year-old Poland international was not impressed after Carlo Ancelotti's side, who had already sealed the Bundesliga title, seemingly failed to support his individual aspirations.
"Robert told me that he got no support and that the coach gave no call to help him in the last game to win the top-scorer title," representative Maik Barthel told Kicker .
"He was disappointed as I have never seen him before. He really hoped that the team would support him proactively."
Lewandowski had already expressed his anger over the issue earlier this month.
"It does not hurt anymore, but it did at first," he was quoted as saying by ESPN. "Maybe because I was not completely satisfied with the way my team helped me.
"Immediately after the last game, I felt anger. I was disappointed with my team. That was the feeling I had."