Goals from William Saliba and Gabriel Jesus gave Mikel Arteta’s side a 2-0 lead at the break before Fabio Vieira completed the win in the 54th minute.
Nwaneri, who is 15 years old, came on as a substitute for Vieira in the second minute of stoppage time, the first player under 16 to play in the competition.
The previous youngest player to feature in the league was Harvey Elliott, now of Liverpool, who was 16 years old when he made his top flight debut for Fulham.
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