It's an achievement that places him alongside Cristiano Ronaldo and Lionel Messi as the only players to have won the award at least twice.
Kane scored 36 Bundesliga goals to claim the honour, awarded to the top scorer across Europe's top divisions, matching the tally that also earned him the award two years ago.
Bayern Munich president Herbert Hainer said the striker had joined an elite group of the club's own goalscoring greats.
"Harry Kane stands alongside striking legends like Gerd Muller and Karl-Heinz Rummenigge at FC Bayern," Hainer said, via the club's official website.
Chief executive Jan-Christian Dreesen also praised Kane's impact both on and off the pitch.
"When Harry Kane plays, the whole world watches. He has raised FC Bayern and the Bundesliga to a new level," Dreesen said, adding that the striker's willingness to put the team above personal success set him apart from many of his peers.
Kane scored 73 goals in all competitions for club and country last season, and helped fire England to a bronze medal at this summer's World Cup. He has now scored 147 goals in 146 appearances for Bayern Munich since joining the club, a record that has made him one of the most prolific forwards in the Bundesliga's history despite arriving in Germany relatively late in his career.
The Golden Shoe, first introduced by French publication L'Equipe in 1967-68 and awarded by European Sports Media since 1997, is decided using a weighted points system that favours goals scored in Europe's strongest leagues.
Kane's second award puts him just behind Messi and Ronaldo, who have each won it multiple times, and further cements his status among the continent's most consistent goalscorers of the modern era. He will formally receive the trophy at a ceremony at the FC Bayern Museum on 19 August.