Moukoko, 16 years and 18 days, has broken a 26-year-old record previously held by Celestine Babayaro. The former Nigeria international made his Champions League debut for Anderlecht in a 1-1 draw with Steaua Bucharest on Nov. 23, 1994 at the age of 16 years and 86 days.
Moukoko came on after 58 minutes as a replacement for Julian Brandt with Dortmund, who have already secured qualification to the round of the 16, trailing Zenit 1-0.
Dortmund went on to rally for a group-topping 2-1 victory over Zenit with goals from Lukasz Piszczek and Axel Witsel.
He made history after becoming the youngest ever Bundesliga player at 16 years and one day following his debut in Dortmund's 5-2 win at Hertha Berlin. He has now made three Bundesliga appearances.
Babayaro, who retired from football in 2010, also holds the record for the youngest player to be sent off in a Champions League match.
Germany youth international Moukoko still has over a year left to put his name into the Champions League history books once more by scoring a goal. Record holder Ansu Fati was 17 years and 40 days old when he scored in Barcelona's 2-1 win at Inter Milan on Dec. 10, 2019.
The 16-year-old has remained cool despite the hype which was ignited by 141 competitive goals in 88 appearances for Dortmund's under-17 and U19 teams.
After making his debut against Hertha, he wrote on Instagram: "Nothing can describe that feeling."
Teammate Erling Haaland, told ESPN: "He's the biggest talent in the world right now. He's got a big career ahead of him. I am over 20 years, I am getting old now. That's how it is."