The 23-year-old, who has impressed the Bundesliga this season with 10 goals and seven assists, sustained the injury during the Super Eagles' training camp in Abu Dhabi.
Nice striker Terem Moffi has been called up as a potential replacement, pending approval from the Confederation of African Football (CAF) and his club.
Boniface has joined a growing list of Nigerian players ruled out of AFCON through injury, including Nottingham Forest striker Taiwo Awoniyi, Leicester City midfielder Wilfred Ndidi, and potentially Leicester forward Kelechi Iheanacho who missed the training camp.
Expressing his disappointment on social media, Boniface said he is devastated to miss AFCON, echoing his absence from the U20 Africa Cup of Nations in 2021.
Nigeria, three-time AFCON champions, will begin their Group A campaign against Equatorial Guinea on 14 January, followed by matches against hosts Ivory Coast and Guinea-Bissau.
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