The United Russia party - which backs President Putin - has lost a third of its seats in the Moscow parliament - according to Russian media.
It will be seen as an embarrassing setback for the Kremlin - although the party still retained a slim majority - 26 out of 45 seats - after Sunday's local elections.
Multiple opposition candidates had been excluded from the ballot paper.
That combined with anger over falling incomes and a rise in the pension age triggered the biggest protests in Moscow for nearly a decade, with thousands being arrested over the summer.
Prominent opposition politician Alexei Navalny - one of those excluded - had pushed his supporters to still go out and vote.
(SOUNDBITE) (Russian) RUSSIAN OPPOSITION LEADER, ALEXEI NAVALNY, SAYING: "In general we can say that the 'tactical vote' worked in the country and, for the first time, it worked much better than we had expected.
This was an experiment, and in those cities and regions where it was implemented for the first time, it worked very very well United Russia's popularity is the lowest it's been for more than a decade.
But across the country, the party's candidates for regional governor seemed to have won in 16 districts, including St Petersburg.
(SOUNDBITE) (Russian) UNITED RUSSIA PARTY CHAIRMAN, ANDREY TURCHAK, SAYING: "On the whole, the result (of the election) in the country is more than positive, it exceeded our most optimistic forecasts.
We are entering the final cycle of preparations for the State Duma election in 2021." But the relatively poor results in Moscow will give hope to opposition parties ahead of those national elections.