The Russian side's captain Danny struck late on to seal the Primeira Liga champions' fate in an otherwise scrappy affair at the Stadion Petrovsky on Wednesday.
Needing to better Zenit's 2-0 win at the Estadio da Luz to overturn the head-to-head record between the sides, Benfica enjoyed the majority of the contest's attacking highlights, though they were few and far between.
Zenit now face a winner-takes-all trip to Monaco in a fortnight's time, though Benfica - who saw their captain Luisao dismissed in time added on - are left to rue a fourth season out of five which has seen them drop out of Europe's premier club competition at the first hurdle.
In a rare Zenit attack before the break, Hulk's thunderous free-kick caused havoc in the Benfica penalty area as Julio Cesar could only spill the ball back into danger before eventually recovering.
A moment of poor concentration almost gifted Benfica the lead, Domenico Criscito allowing Eduardo Salvio to steal in at the back post from Nico Gaitan's cross, but Zenit goalkeeper Yuri Lodygin was sharp to bail out the Italian.
Benfica came roaring out for the second period and could have taken the lead twice within 15 minutes of the restart, but Luisao wastefully skewed an effort wide when one-on-one before Gaitan's persistence to get to the byline and fire across the six-yard box was not rewarded by a supporting colleague.
The Hulk-Danny combination swapped roles soon after though to fine effect as Zenit claimed the points.
