An exit poll by the Public Opinion Foundation showed Sobvanin earned 52.5 percent of the vote over opposition leader Alexei Navalny's 29.1 percent, though VTsIOM, a state-run pollster, said Navalny drew 32 percent.
Ivan Melnikov, a Communist Party candidate, came in third with 8 percent, the Public Opinion Foundation said.
About 50 percent of Moscow's voters had been expected to vote Sunday, and the turnout proved low for the city's first mayoral election in a decade, RIA Novosti reported. The final tally of voters was not reported.
Political observers expected Sunday's election to provide a clue to Russian President Vladimir Putin's popularity. Sobvanin is an ally of Putin and had been expected to win easily.
Navalny had an unexpectedly strong turnout, RIA Novosti said.
Boris Makarenko, chairman of the Center for Political Technologies, predicted a strong turnout for Navalny could indicate a level of public dissatisfaction with the administration of President Vladimir Putin.
"A sizable part of the vote against Sobvanin will be against not the Moscow city government or the personality of the Moscow mayor, but against federal politics," Makarenko said before the election. "The Kremlin is receiving many signals that a sizable part of the population has problems with how it is governing the country."