Jonas Hofmann opened scoring for the home team in the 22nd minute.
The home team doubled their advantage 10 minutes later through Jeremie Frimpong.
Boniface scored Bayer Leverkusen third goal of the game in the 67th minute.
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The 22-year-old has now scored seven goals in seven league appearances for Die Werkself this season.
Xabi Alonso’s side maintained top spot on the table with nine points from seven goals.
Boniface is in third position on the top scorer’s chart.
Only Stuttgart forward Serhou Guirassy and Bayern Munich’s Harry Kane have scored more goals than the Nigeria international in the Bundesliga this season.
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