Hulk put the visitors 1-0 up after five minutes and things quickly went from bad to worse for Benfica, whose keeper Artur was sent off, before Witsel doubled the lead with a header midway through the first half.
Zenit are joined at the top of Group C on three points by Monaco who beat Bayer Leverkusen 1-0.
Zenit coach Andre Villas-Boas named arguably his strongest side with central defender Ezequiel Garay and midfielders Witsel and Javi Garcia lining up against their former club.
Zenit had a chance to open the scoring in only the second minute as Hulk unleashed a dangerous strike across goal which Oleg Shatov was just inches away from turning into the net.
It was not long before the away fans were celebrating, however, as Hulk finished with aplomb after being picked out by an excellent pass from Shatov.
Zenit had a chance to double their lead on 10 minutes as Hulk hit a free kick, which goalkeeper Artur could only parry, before the keeper received his marching orders eight minutes later for bringing down Danny outside the penalty area.
Paulo Lopes was brought on to replace him and one of his first tasks was to pick the ball out of the net as Witsel rose highest in the penalty area to head home a corner.
Benfica had an opportunity to reduce the deficit after the break as Luisao went close with a header, but Zenit goalkeeper Yuri Lodygin showed good agility to save.
Hulk could have killed the game off a minute later, but his shot from an acute angle hit the post, while Jose Rondon also had a chance after being put through on goal, yet was unable to find the back of the net.
Zenit will host Monaco on Oct. 1 when Benfica will visit Bayer Leverkusen.
(Reporting By Dmitriy Rogovitskiy; editing by Toby Davis)
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