The Nigeria international, alongside Nathan Tella, was introduced with 10 minutes remaining at St James’ Park.
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Leverkusen took an early lead through Ibrahim Mazda in the opening minute, but the Magpies responded just before half-time, with Malick Thiaw restoring parity.
Boniface then produced a decisive moment in the 82nd minute, dribbling past his marker before calmly slotting the ball beyond the goalkeeper to seal victory for the Bundesliga champions.
