The judge rejected Navalny's claims that the campaign was marked by abuse of government finances and selected voter fraud, ruling that there were no grounds for a recount.
Navalny's success in the elections proved an embarrassment to his Kremlin-backed opponent, incumbent Sergei Sobyanin.
Sobyanin got 51 per cent of the vote, just avoiding the 50 per cent cut-off that would have forced him into a second round against Navalny.
Independent election monitor Golos also criticized the election result, saying that there had been no evidence of widespread vote-rigging but that isolated violations could have tipped the close election.
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He left the courtroom in handcuffs, but a day later in a surprise turnaround, prosecutors requested he be set free until the sentence was approved on appeal.
Most have speculated that it was Sobyanin who had Navalny set free, in order to ensure that the elections would look fair and competitive, giving legitimacy to the Kremlin candidate.
The opposition activist's strong showing at the polls could be reflected in the appeal case, as his growing publicity and proven popularity could make it riskier than before to put him behind bars.
When Navalny was first convicted, several thousand people filled the streets of Moscow to protest the court's decision.
Navalny will contest both the verdict and the sentencing of the trial. But even if the sentence is reduced or if he receives a suspended sentence, anything but an innocent verdict rare in Russia's judicial system would disqualify him from running for political office according to Russian law.