Andre Villas Boas' side are unbeaten in the league this season and recorded a 10th win of the campaign thanks to Javi Garcia's early strike at the Arena Khimki on Saturday.
The Spaniard's goal came just seven minutes into Saturday's clash as he reacted quickest after Axel Witsel's header had come off the post.
Zenit found themselves holding on towards the end, with Alan Dzagoev going closest with an deflected agonisingly wide, but managed to ride out the storm and claim a crucial three points.
Luckily for CSKA, their advantage in second place remains four points after Krasnodar were surprisingly beaten 2-1 at Mordovia Saransk on Sunday.
Joaozinho had given Krasnodar the lead seven minutes before half-time, but Oleg Kononov's side were defeated by a second-half brace from Marko Lomic.
Terek Grozny moved into fourth place with victory over Ufa on Monday, Jeremy Bokila's strike on the stroke of half-time sealing the win.
Spartak Moscow's wait for a league win now stands at five games after they were held to a 3-3 draw at Kuban Krasnodar - Ivelin Popov's 68th-minute penalty earning a share of the spoils for the hosts.
Two other Moscow sides met on Sunday, with Lokomotiv inflicting a 4-2 defeat on Dinamo - who had led 2-0.
After 50 minutes, the points appeared to be going to Dinamo thanks to goals from Alexei Ionov and Balazs Dzsudzsak, but four goals in 27 minutes gave Lokomotiv bragging right.
Roman Pavlyuchenko completed the victory with five minutes to play after Dame N'Doye, Alexander Samedov and Alan Kasaev had turned things around.
At the bottom, it was 12th time lucky for Arsenal Tula as they finally recorded a first league win of the season, beating fellow strugglers Torpedo Moscow 1-0 to close the gap between the two sides to just one point.
Rostov moved themselves out of the bottom two with a 1-0 win over Ural, while Amkar Perm held Rubin Kazan to a 1-1 draw thanks to Branko Jovicic's last-minute leveller.
