The prodigious striker lashed home a rocket of a shot from just inside the penalty area to draw Dortmund level at Alten Forsterei after Taiwo Awoniyi had put the host in front after 57 minutes.
🔥🔥🔥 #YoussoufaMoukoko became the youngest goalscorer in #Bundesliga history today with this spectacular bomb 💥 But it wasn't enough to earn a win for an increasingly desperate @BVB 😬 More here ▶️ https://t.co/X05EWDDnR6 | #FCUBVB | #UnionBVB | @bet365 pic.twitter.com/pnLPhrYVW5— beIN SPORTS (@beINSPORTS_AUS) December 18, 2020
His goal ultimately proved in vain as Marvin Friedrich quickly restored Union's' lead to secure a 2-1 win, but at just 16 years and 28 days Moukoko sets a new German top-flight benchmark.
It surpasses the record set by Bayer Leverkusen youngster Florian Wirtz, who was 17 years, one month and three days when he scored his first Bundesliga goal in June.
Moukoko had already become the youngest player to appear in the Bundesliga after coming off the bench against Hertha Berlin the day after turning 16 last month in a 5-2 win.
He was named in Dortmund's starting XI for the first time in the midweek clash against Werder Bremen, a 2-1 victory in Edin Terzic's first match as head coach.
Earlier this month, Moukoko became the youngest player to appear in the UEFA Champions League.
He came off the bench in a 2-1 win at Zenit after 58 minutes, with his 16 years and 18 days old beating the 16 years and 87 days of Celestine Babayaro during the 1994-1995 UEFA Champions League group stages for Anderlecht.
Moukoko's delight, though, was short-lived as Dortmund again conceded from a set-piece as Union centre-back Marvin Friedrich headed the winner from a corner with 12 minutes left.
Last weekend's 5-1 thrashing at home to Stuttgart cost former head coach Lucien Favre his job, but Dortmund's defensive woes were exposed again by Union, which also beat it 3-1 in eastern Berlin last season.
Despite bouncing back in mid-week with a 2-1 win at Werder Bremen under caretaker coach Edin Terzic, Dortmund was again punished for yielding possession easily and sloppy defending from corners.
This is Dortmund's fifth defeat this season, leaving it fourth in the table, six points behind Bayer Leverkusen, which hosts Bayern Munich in Sunday's (AEDT) top-of-the-table clash.
Union, which held Bayern Munich to a 1-1 draw in its previous home game, climbs to fifth, just a point behind Dortmund.
It deservedly took the lead behind closed doors when Awoniyi slipped his marker Giovanni Reyna and headed past Dortmund goalkeeper Roman Buerki on 57 minutes.
Having previously hit the Union woodwork, Moukoko made history three minutes later when he stabbed home the equaliser, but Friedrich was left alone in the area to head the winning goal in off the post.
The Bundesliga starts a two-week winter break after this weekend and Dortmund has a tough month ahead in January when it faces RB Leipzig, Bayer Leverkusen and Borussia Moenchengladbach.
However, Moukoko clearly has a bright future after now claiming three records in the last month.