If Kevin Faulconer holds his lead, San Diego would be the nation's largest city with a Republican mayor. He would be the only Republican to lead a major city in California, where Democrats hold all statewide offices.
With 238,000 ballots counted, Faulconer led Democratic Councilman David Alvarez by 55.2 per cent to 44.8 per cent. Many expected a much closer contest.
Faulconer, 47, stopped just short of declaring victory, promising, as he has throughout the campaign, to work across political party lines in an increasingly Democratic city.
"I can't wait to be the next mayor of this fabulous and great city," he told supporters.
Alvarez, 33, sought to become the first Latino mayor in the city's 164-year history and keep Democrats in an office that Filner won in 2012 after a 20-year absence for the party. He campaigned by saying the city has been run by an elite few.
"While we do not know the final outcome yet, this much is clear: We have changed San Diego," Alvarez told supporters.
Faulconer portrayed Alvarez as a tool of labour unions. Alvarez attacked Faulconer as a shill for corporate interests.
Despite sharp ideological differences, few issues separated the candidates. Both promised more attention to neighbourhood priorities like street repairs, library hours and emergency response times, putting less emphasis on ambitious civic projects like building a new City Hall and bringing a new stadium for the NFL's Chargers.
Filner, 71, embraced the same "neighbourhoods-first" mantra but Faulconer and Alvarez scarcely mention the disgraced former mayor, who pleaded guilty in October to one felony count of false imprisonment and two misdemeanour counts of battery. The former 10-term congressman began a three-month sentence of home confinement on Jan. 1.
Faulconer, who was backed by Filner's two-term Republican predecessor, Jerry Sanders, played down his party affiliation. He highlighted his opposition to a 2010 ballot measure to raise the sales tax, which lost resoundingly, and his support for a 2012 measure to cut pensions for city workers, which passed overwhelmingly. Alvarez backed the losing sides.
Faulconer's strong early showing comes as the nation's eighth-largest city turns more Democratic. President Barack Obama defeated Mitt Romney by 25 percentage points among city voters, and Democrats enjoy a 13-point advantage over Republicans among registered city voters.
The San Diego County registrar of voters predicted turnout between 45 per cent and 50 per cent, higher than the 36 per cent turnout in a first round voting in November. The first batch of results amounted to about half of the expected turnout.
Faulconer easily topped a field of 11 candidates in the first round by dominating in newer, wealthier neighbourhoods north of Interstate 8. Alvarez secured a spot in Tuesday's runoff by cleaning up south of the freeway in more densely populated, predominantly Latino areas.
Faulconer, a former public relations executive, was elected to the Council in 2006 after another mayor, Dick Murphy, resigned amid a crisis over city finances. He often recalled how the city weathered the turmoil, drawing a contrast with the less experienced Alvarez, who was elected to the Council in 2010.
Alvarez, a former legislative aide who grew up speaking Spanish at home, extolled his family's immigrant roots to an electorate that the registrar estimates is 18 per cent Latino. He embraced a populist campaign theme of stripping power from hoteliers and developers who he says have long controlled the city.