In 2013, Sobyanin barely escaped a second-round run-off after a strong challenge from protest leader Alexei Navalny, winning 51.4 percent of the vote, with Putin's top critic unexpectedly picking up over a quarter of the ballots.
This time round serious opposition candidates were kept off the ballot paper in favor of the incumbent.
In a nationwide day of polls, members of the ruling United Russia party also won in elections for governors and lawmakers in other Russian cities.
Police arrested 1,018 people, mainly in Saint Petersburg and the Urals city of Ekaterinburg, who were taking part in demonstrations in dozens of Russian cities, independent monitor OVD-info said.
In Moscow, police opened two criminal probes over violence against representatives of the authorities, the monitor said.
Government plans to raise the state pension age to 60 for women and 65 for men has led to a rare outburst of public anger and seen Putin's approval ratings take a major hit.
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