The two sides played out an uninspiring goalless draw in a game that saw the hosts' Belgian midfielder given his marching orders.
Hulk came closest to breaking the deadlock after seeing his low drive cannon off the post, before Axel Witsel was shown a contentious red card in the 44th minute at the Stadion Petrovskij after Zenit had dominated the first half.
Witsel's dismissal allowed Vienna to have more of the ball in the second period, and Marin Leovac had a goal ruled out with the goalkeeper adjudged to have been fouled in the build-up.
Luciano Spalletti named Andrey Arshavin among the Zenit substitutes after the former Arsenal forward featured in Saturday's 4-2 triumph over Spartak Moscow.
Zenit dominated the opening exchanges with Hulk particularly threatening. The Brazil international controlled a throw-in in the 12th minute before turning sharply and flashing a first-time effort against the post.
And he continued to give the away side problems when he cut in from the left-hand side of the box and fired across goal to force Heinz Lindner into a smart save.
Vienna responded by nearly sneaking ahead on the 30-minute mark. Tomas Simkovic floated a corner to the back post and James Holland put a free header wide. Aleksandr Kerzhakov then missed a golden opportunity for Zenit. In a 2-on-2 situation, Hulk drove at the defense and slipped a through ball to the Russia international who sliced his left-foot effort wide.
The visitors then had a chance of their own as the Zenit defense retreated shortly after, allowing Philipp Hosiner to drag a 20-yard effort wide of the post.
The talking point of the half arrived on the stroke of halftime when Witsel was shown a controversial red card for a sliding tackle on Mader that looked to have caught his ankle.
Vienna looked to make the most of the extra-man advantage after the break as Leovac had a goal ruled out in the 52nd minute following Daniel Royer's collision with goalkeeper Yuri Lodigin.
Nenad Bjelica's side continued to press, and substitute Thomas Murg should have done better on the hour mark when he blazed over from the edge of the box.
With 20 minutes remaining, Hulk once more came close for Zenit, but his powerful free kick flew narrowly wide of the target.
Vienna nearly claimed a dramatic win late on when Hosiner headed Simkovic's cross wide, but the result leaves both sides still searching for their first win in this season's competition.