Zenit did not take long to take advantage of a lacklustre start by the visitors. A fine pass by Oleg Shatov in the third minute was played in Artem Dzyuba, who had time to take a touch before stroking the ball past Anthony Lopez to score his 11th goal in as many games for club and country.
Andre Villas-Boas' side were dominant and should have extended their lead. Dzyuba had a great chance to score his second following good work by Shatov and Hulk, but he slipped at the vital moment and his shot ballooned over the bar.
Whatever Hubert Fournier said to his team at half time worked, as they were rejuvenated. The French outfit drew level four minutes after the break as Alexandre Lacazette brilliantly deflected Christophe Jallet's cross past Mikhail Kerzhakov.
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Lyon looked to be dominating but Hulk scored a stunning goal in the 56th minute to put the hosts back in front. The Brazilian forward picked the ball up on the halfway line and advanced towards the Lyon goal before unleashing an outstanding left foot shot which swerved past Lopez to score his third goal in as many Champions League games this season.
Dzyuba missed another glorious opportunity to put Zenit 3-1 ahead as he shot wide after being put though on goal. Lyon pushed forward in search of an equaliser and Lacazette almost provided it, but he was denied by an excellent last-ditch tackle by Alexander Anyukov.
With nine minutes to go, Lyon were caught on the break and Zenit captain Danny sealed victory with a composed finish after being played in by Shatov.
Zenit stay top of Group H with nine points from three games, while Lyon have just a point. The two sides meet again in France on Nov. 4 in a game Lyon have to win to keep their qualification hopes alive.
(Reporting By Dmitriy Rogovitskiy, editing by Pritha Sarkar)
