Faulconer, 47, said Wednesday that he was surprised by the "overwhelming" margin of victory. As he did throughout the campaign, he played down his party affiliation in an increasingly Democratic city.
"It's not about if you're a Republican, a Democrat or independent. We want a mayor that's going to stand up for San Diego and bring us all together. It's not partisan; it's about leadership," he told KNSD-TV.
Alvarez, 33, congratulated Faulconer late Tuesday, tweeting, "It's clear that he will be the next Mayor of San Diego. I look forward to working with him."
Faulconer portrayed Alvarez during the campaign as a tool of labor unions. Alvarez, who sought to become the city's first Latino mayor, attacked Faulconer as a shill for corporate interests.
Despite sharp ideological differences, few issues separated the candidates. Both promised more attention to neighborhood 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 "neighborhoods-first" mantra but the candidates scarcely mentioned the disgraced former mayor, who pleaded guilty in October to one felony count of false imprisonment and two misdemeanor counts of battery. The former 10-term congressman began a three-month sentence of home confinement on Jan. 1.
Faulconer alluded to the scandal when addressing supporters Tuesday night, saying, "We know that this city has gone through a lot in the last year but we knew as San Diegans we were better than that."
Faulconer, who was backed by Filner's two-term Republican predecessor, Jerry Sanders, 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, a former student body president at San Diego State University, 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.
Faulconer's win 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.
Faulconer easily topped a field of 11 candidates in the first round by dominating in newer, wealthier neighborhoods 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.
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 percent Latino. He embraced a populist campaign theme of stripping power from hoteliers and developers who he says have long controlled the city.