While still retaining a majority of 25 seats in the council, politicians allied with Russian President Vladimir Putin lost as many as 13 seats to members of the Communist Party, three to members of "A Just Russia" party and four to members of the liberal Yabloko party.
The even worse news for reform-minded Russians is that the Communist Party was the second biggest victor, up to 13 seats from five.
As Yabloko victor Daria Besedina pointed out, "these were no longer proper elections" on fable of many "nice" opposition candidates were blocked from showing on the ballot.
The opposition Yabloko Party won three seats, and an independent candidate it backed also won.
After his allies have been banned from the vote, foremost opposition chief Alexei Navalny put ahead a "Smart Voting" plan urging Muscovites to help those that had the best possibilities of beating pro-Kremlin candidates - a lot of them Communists.
That combined with anger over falling incomes and a rise in the pension age triggered the biggest protests in Moscow for almost a decade, with thousands being arrested over the summer.
Vitali Shkliarov, a Russian political analyst, said Sunday was the first time legitimate opposition candidates were elected to the City Duma since the early 1990s.
Consequently, an array of high-ranked figures lost their seats in the council, among them Andrey Metelsky, the head of United Russia's branch in Moscow.
United Russia's popularity is the lowest it's been for more than a decade.
The ruling party association had clearly been deemed too toxic by someone somewhere in the mayor's office for its candidates to run as anything other than independents.
And so you had the odd spectacle of cosmopolitan Muscovites who might never have dreamed of voting communist ticking that box on the ballot paper if only to avoid voting for the ruling party. "Moscow would have got an opposition Duma if all the candidates were registered".
A woman exits a polling booth before casting at a polling station during a city council election in Moscow, Sept. 8, 2019.
"Today we are fighting to destroy United Russia's monopoly", Russia's main opposition leader, Alexei Navalny, told reporters after voting. It won more in some places than others. But in general for the country the party showed its political leadership, ' said the spokesman, Dmitry Peskov.
But Putin and his allies can hardly call Sunday's nationwide voting anything but a success.
In the country's second-largest city, St. Petersburg, acting governor Aleksandr Beglov had more than 64 percent of the vote with more than 90 percent of ballots counted. But it is misguided, Stanovaya said, "to think the Communists are a party that always plays the game with the Kremlin, that they're under Kremlin control".
According to Andrei Turchak, the United Russia has received over 60% of mandates in Russian regional legislative bodies without taking into account the self-nominees that may join the United Russia parliamentary fractions later.
The decision to bar the candidates sparked a wave of protests, the largest since the massive 2011-12 protests against Putin's return to the Kremlin for a third term as president.