Daniel Milicevic scored a left-footed winner 12 minutes from time to secure the points for Ghent after Laurent Depicter had put them ahead at halftime, only for Artemis Dzyuba to equalise in the 65th minute.
Ghent matched the achievement of Underlet in the 2000-01 season by finishing second in the group, ending with 10 points behind Zenit who amassed 15.
Depicter, recently capped for the first time by Belgium, headed the home team ahead in the 18th minute, connecting powerfully with Moses Simon's cross after rising above Zenith's Belgian international defender Nicolas Lombard's, who had began his career at Ghent a decade ago.
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Depicter should have had a second just after the half-hour mark when a stray back pass from Luis Net fell perfectly for the centre forward to run onto but as he bore down on the goalkeeper an outstretched leg from Yuri Lodging rescued Zenit. There were several occasions in both halves where Ghent's defending looked nervy and ultimately it saw them cede their lead when the failure by both Seven Kumis and Lasses Nielsen to clear an innocuous-looking cross set up Dzyuba.
It was the sixth goal in the group phase for the Russian international.
Yet the crowd at the Ghent Stadium exploded back into life once more when the Swiss-born Milicevic restored the lead.
(Reporting by Mark Gleeson; Editing by Ed Osmond and Ian Chadband)
