The Nigerian forward registered his second consecutive goal for the Iron Ones to help his side edge past Edin Terzic’s men
Awoniyi teamed up with the Stadion Alte Foersterei outfit in the summer on a season-long loan from Premier League side Liverpool.
The Nigerian forward was handed his eighth league start and made the most of the opportunity to score his second consecutive goal for the Iron Ones.
Cameroon forward Moukoko also opened his goal account for the Black and Yellows, becoming the youngest goalscorer in the division.
Awoniyi put Union Berlin in front in the 57th minute following an assist from Grischa Proemel after both sides failed to break the deadlock in the first half.
Moukoko then levelled proceedings three minutes later after receiving a timely assist from Raphael Guerreiro.
Marvin Friedric then sealed the victory in the 78th minute to help Union Berlin bounce back to winning ways after a four-game winless run.
Awoniyi featured for 86 minutes before he was replaced by Akaki Gogia while Moukoko played for the duration of the game.
With the result, Union Berlin moved to fifth on the Bundesliga table after gathering 21 points from 13 games.
Borussia Dortmund, meanwhile, dropped to the fourth spot with 21 points from the same number of matches.
Awoniyi has now scored four goals and provided one assist in 11 appearances for Union Berlin since his arrival at the club.
The forward will hope to continue his impressive form in front of goal when his side take on Paderborn in a DFB Pokal tie on December 22.
Awoniyi has represented Nigeria at the U17, U20 and U23 but he is yet to get a chance to feature for the Super Eagles.
The forward recently revealed he would continue to give his best for his club while hoping to get a call-up to the national team.