Having earlier hit the woodwork in Berlin, Moukoko leapt into the air in celebration after firing home an equaliser after Liverpool loanee Taiwo Awoniyi had given Union the lead early in the second half.
Moukoko breaks the previous record of Leverkusen's Florian Wirtz, who was 17 years, 34 days when he scored against Bayern Munich in June.
This is the third record Moukoko has claimed in the last month.
He became the Champions League's youngest player in early December, coming off the bench in the win at Zenit St Petersburg with Dortmund through to the last 16 where they face Sevilla.
He also became the youngest player in Bundesliga history on November 21 -- the day after his 16th birthday.
ryj/td