Zenit went ahead in St. Petersburg in the 25th minute, Konstantin Zyrianov finishing a piercing run with a powerful shot. However, the Russian champions and UEFA Cup holders were unable to add to their lead, and two well-taken goals in five minutes by Maxim Buznikin and Ricardo Silva, in the 52nd and 57th minutes respectively, put the Yaroslavl-based club ahead.
Zenit, who had welcomed back striker Pavel Pogrebnyak after a two-month injury lay-off, hit back, searching for the equalizer, but were caught on the break by Shinnik in the 79th minute, with Dmitry Kudryashov racing away to fire home.
The St. Petersburg club are now in 7th place, 11 points behind Rubin.
The win lifted Shinnik off the bottom of the table.
Rubin FC followed on from their 4-1 defeat of Zenit last week by beating Tom Tomsk 2-1 away from home, a superb goal by ex-Tottenham Hotspur striker Sergei Rebrov in the 32nd minute giving his side all three points.
Dynamo Moscow, who beat Spartak Nalchik 1-0 in the Russian capital, remain two points behind the Kazan side.
Spartak Moscow drew 1-1 away to Amkar. The match was their first since the club's manager, Stanislav Cherchesov, was sacked last week following the team's 4-1 defeat at home to Dynamo Kiev in the Champions League. Amkar, from the Siberian city of Perm, remain in third place, ahead of Spartak on goal difference.
Weekend results -
Zenit St. Petersburg 1 Shinnik 3
CSKA 2 Terek Grozny 0
Amkar 1 Spartak 1
Dynamo Moscow 1 Spartak Nalchik 0
Khimki 0 Moskva 2
Lokomotiv 0 Saturn 0
Luch-Energiya 0 Krilya Sovetov 0
Tom Tomsk 1 Rubin 2
Table (all 18 games unless otherwise stated).
Rubin - 36
Dynamo Moscow - 34
Amkar - 29
Spartak Moscow - 29
CSKA Moscow -28
Krilya Sovetov -27
Zenit -25
Lokomotiv Moscow (17 games) - 25
Spartak Nalchik - 24
Moskva - 22
Terek Grozny - 21
Tom Tomsk - 19
Saturn - 18
Luch Energiya - 17
Shinnik (17 games) -14
Khimki - 13
