Signal Iduna Park is rarely short of colour, and Zenit fans enlivened proceedings when they torched the Bundesflagge und Handelsflagge as their side went out.
Zenit midfielder Tomáš Hubočan also suffered a bloody injury late on following a clash with Robert Lewandowski, and was left nursing a large gash.
Zenit fans burn a German flag inside Signal Iduna Park
With a 4-2 away win in the bank from three weeks ago, Borussia held almost all of the cards and played them conservatively to secure their passage even as they lost 2-1 on home soil.
Zenit's new manager is former Spurs boss André Villas-Boas
Hulk's 16th-minute wonder strike for Zenit was cancelled out by Sebastian Kehl seven minutes before half-time, and although Zenit substitute Rondon scored a second with 17 minutes to go, there was little threat of them getting back on level terms.
Dortmund v Zenit
The only significant negative for Jürgen Klopp was a yellow card for star striker Robert Lewandowski, ruling him out of their next match.