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Juventus forward Ronaldo also made history as he became the first player to finish as top scorer in the Premier League, La Liga and now Serie A. But his total of 29 was not enough to catch Lewandowski.
Messi, who missed Barcelona's final game of the season on Saturday as he was given extra time to rest ahead of the Copa America tournament, finished the campaign on 30 goals as the leading scorer in La Liga.
The award is given on a points basis with a player's goals total multiplied by two, 1.5 or one based on the strength of their leagues. Players from the Premier League, La Liga, Serie A, Bundesliga and Ligue 1 have their goals total multiplied by two, giving Lewandowski a points tally of 82.
Lewandowski failed to score in only four of the 27 league matches he started for Bayern this term. He scored three or more goals on five occasions. His nearest challengers in the Bundesliga were Borussia Dortmund's Erling Haaland (27) and Eintracht Frankfurt's Andre Silva (28).
With 276 goals, Lewandowski is 89 behind Muller's all-time Bundesliga record and has averaged nearly 28 goals a season since joining Dortmund in 2010.
Under contract at the Allianz Arena for another two years, Lewandowski could now target the all-time record for which he would likely require another deal at Bayern.
This is Lewandowski's first Golden Shoe. Messi has the most with six, and his total of 50 in the 2011-12 campaign remains the highest single-season tally.