In a mayoral election that tested the Kremlin’s strategy against its opposition, and that brought some of the divisions within the Kremlin itself close to the surface, charismatic anti-corruption Moscow mayoral candidate Alexei Navalny made a far stronger showing than expected Sunday.

Incumbent Mayor Sergei Sobyanin, a close ally of President Vladimir Putin, won 51.32 percent of the vote and Navalny 27.27 percent, the Moscow election commission said, in a count based on 99.6 percent of polling stations reporting. The result almost guarantees a shift in the Russian political landscape.

But Navalny, who rose to prominence after widespread vote-rigging in a 2011 election, said Sunday night he was sure that the figures were cooked behind closed doors. He called on the Kremlin — rather than City Hall — to admit that the race should go to a runoff.

Navalny had spent the entire campaign running not against his leading opponent, Sobyanin, but against President Vladimir Putin — and that strategy appears to have clicked with a large number of voters.

“We don’t know him very well,” said Lyuba Kulikova, a Navalny voter in the historic center of Moscow. “But we know he’s fighting against them,” said her husband, Alexei, referring to Putin’s United Russia party.

Navalny memorably dubbed United Russia the “party of crooks and thieves,” and the sobriquet stuck.

A citizens group that was collecting results precinct-by-precinct said midnight Sunday that Sobyanin had fallen below the 50 percent mark.

Navalny’s final tally is still a much better showing for him than any poll had predicted even a week ago, and it left two big questions hanging over Moscow.

Although Sobyanin barely squeaked through in the first round, has his standing been weakened, especially among his colleagues? And, more importantly, what does such a showing mean for Navalny, the star of last year’s protest movement?

Navalny is free on appeal following his July conviction on embezzlement charges and being sentenced to five years in prison in a case that was widely viewed as trumped up. His supporters argue that winning the votes of so many Muscovites will ensure that authorities allow him to remain free.

Navalny’s release the day after he was sentenced — almost certainly on the Kremlin’s orders — was seen as an attempt to ensure that Sobyanin would have legitimate opposition and could then declare himself a legitimately elected mayor, once his inevitable victory was cemented. Navalny’s release was reported as a victory for the more liberal factions of Putin’s inner circle over the hard-liners who wanted to see the opposition star go straight to prison.

Sobyanin resigned in the spring to bring on the quick election, and Putin immediately appointed him acting mayor to run the city until election day. The idea behind the truncated election season was that Navalny and Sobyanin’s other opponents would have little time to put campaigns together. But Navalny launched a strategic citywide campaign, heavily focused on volunteers and Internet advertising, that seemed to catch the Kremlin off guard.

However, Sunday’s turnout was low. Two hours before the polls closed, only 26 percent of eligible voters had cast ballots. The final result may be barely more than half the number of those who voted in the 2012 presidential election.

Some irregularities were reported to the Golos election-monitoring organization, but there were none of the blatant abuses that launched the political protest movement after the 2011 parliamentary election. Navalny’s supporters warned against abuse of balloting at the homes of people with disabilities, which is harder to monitor, and irregularities during the counting of votes.

Of the four other candidates, only one, Ivan Melnikov, the Communist Party standard-bearer, had won a significant number of votes, according to exit polls that showed him with 8 or 9 percent of the vote.

Sobyanin, who is from northern Siberia, was appointed mayor in 2010. His gamble in seeking an election in 2013, a year ahead of schedule and the first in Moscow in a decade, may have backfired, even in victory. And it may cause deeper ruptures in the circles around Putin, where opinions about how to deal with Navalny and the university-educated opposition are apparently diverging.

The citizen watchdog organization reported that Sobyanin had gotten his best results in the working-class regions of southeast and northeast Moscow.

Navalny was strongest in the center and in fashionable southwest Moscow — where education levels and incomes are higher — this despite Sobyanin’s stated goal during the past year that he must find ways to retain Moscow’s “creative class” in order to make it a more vibrant city.

In another race, far from the cafes of Moscow’s Boulevard Ring, the political opposition received seemingly good news in the Ural Mountains city of Yekaterinburg, Russia’s fourth-largest city. There, the popular but controversial founder of a drug-treatment foundation, Yevgeny Roizman, was leading in the mayoral race, with half the votes counted — according to the local election commission.

But then the central election commission mysteriously announced that Roizman was significantly behind, with no explanation.

Roizman is allied with Mikhail Prokhorov, the billionaire owner of the NBA’s Brooklyn Nets who has been dabbling in politics since the summer of 2011.

Prokhorov’s most prominent provincial ally, Yevgeny Urlashov, was arrested in the spring just a year after being elected mayor of Yaroslavl, and is currently being held without bail on charges that he, like Navalny in his case, claims are politically motivated and without foundation.

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