Nwaneri came off the bench late on as the Gunners returned to the top of the table with a 3-0 win at Brentford.
He broke the record previously held by Liverpool's Harvey Elliott when he appeared for Fulham aged 16 years and 30 days. Nwaneri also set a new landmark for the youngest Arsenal player in any competition that was held by Cesc Fabregas.
Nwaneri had been expected to spend the season with Arsenal Under-18s but he was quickly promoted to the Under-21s following his impressive performances.
Injuries to captain Martin Odegaard and Oleksandr Zinchenko had left Arsenal boss Mikel Arteta short of midfield options.
"It was a pure gut feeling," said Arteta on handing Nwaneri a debut.
"Yesterday he had to come because we have injuries, especially the injury of Martin and then I had that feeling from yesterday that if the opportunity could come that I was going to do it."
Northern Irish schoolboy Christopher Atherton became the youngest senior footballer ever in the United Kingdom earlier this week when he appeared for Glenavon aged 13 years and 329 days.
