Michael Heselschwerdt, the head of UEFA club competitions, conducted the draw in the absence of Gianni Infantino - who was in Zurich for the presidential election.
Heselschwerdt was joined by former BVB forward Alexander Frei. He scored 34 goals in 74 games, including four goals and three assists in five games against Schalke 04.
Dortmund tasked with in-form Spurs
Despite what could be looked on as a good omen, Frei was unable to give his former side a favourable draw.
They will face the side that currently sit second in the Barclays Premier League, Tottenham Hotspur. This also means a reunion with old foe, Heung-Min Son.
The South Korean international seemed to be at his best when facing BVB, though his playing time hasn't been the same since moving from Leverkusen in January.
Dortmund will hosts Mauricio Pochettino's men at the Westfalenstadion in the first leg, before traveling to White Hart Lane for the return fixture.
Leverkusen paired up with Villarreal
One of the most intriguing ties of the round sees Leverkusen square off against a very impressive Villarreal side.
The Yellow Submarine are sitting comfortably in fourth in La Liga, and are just six points behind second-place Atlético Madrid.
Die Werkself will be hoping to exact revenge for their defeat to Villarreal at the same stage in the 2010/11, losing out 5-3 on aggregate.
Both German teams will be facing a battle to qualify, although the pair will most definitely fancy their chances of progressing into the quarter-finals.
The UEFA Europa League last sixteen draw in full
Shakhtar Donetsk v Anderlecht
Basel v Sevilla
Villarreal v Bayer Leverkusen
Athletic Club v Valencia
Liverpool v Manchester United
Sparta Praha v Lazio
Borussia Dortmund v Tottenham Hotspur
Fenerbahçe v Braga
Ties to be played on March 10th and 17th.