Dieumerci Mbokani finished off a superb team move in the first half to settle the clash in Brussels, leaving the visitors on the brink of exiting European competition this season.
The Congo striker combined superbly with American midfielder Sacha Kljestan to settle a tense match in Brussels, as the Russian side struggled to create any chance of note in the absence of Brazil international Hulk.
Anderlecht surprisingly elected to leave Tom De Sutter on the bench despite his recent form in front of goal, with Mbokani starting as the lone striker in his stead. Mbokani was presented with the first opening of the match after less than a minute, when Milan Jovanovic's cross was missed by Tomas Hubocan and slmost bounced kindly for the striker, but he was unable to bring it under control.
Anderlecht continued to look the brighter of the two sides in the opening exchanges, and, just past the 15-minute mark, Mbokani justified his selection with a superbly-taken goal, linking up with Kljestan on the edge of the box before chipping the ball over Vyacheslav Malefeev to notch his side's first goal in four games in the competition this season.
Zenit began to get a foothold on the ball but was unable to make any real attacking headway, with Axel Witsel's booking for a clumsy challenge an embodiment of the frustration within the Russian ranks.
Luciano Spalletti brought on Danny at the break to spark some life into his attack, and the 29-year-old almost had an immediate impact when his dangerous free-kick fell to the feel of Witsel, only for Anderlecht goalkeeper Silvio Proto to deny the Belgian with a smart save.
Chances were few and far between for the remainder of the match, with Anderlecht all too often winning the battle in midfield to prevent the visitors from making any real headway in the final third while the center back duo of Kouyate and Bram Nuytinck as immense at the heart of the hosts' defense.
Anderlecht trails AC Milan by one point for second place in Group C ahead of their clash in two weeks' time, while Zenit sits in last place, still within range but in need of help in the remaining two games, trailing Milan by two points and Anderlecht by one.