Faulconer is expected to be sworn in as mayor on March 3. San Diego will become the nation's largest city with a Republican mayor, and Faulconer will be the only Republican to lead a major city in California, where Democrats hold all statewide offices.
With all precincts reporting, the two-term councilman and former public relations executive led Democratic Councilman David Alvarez by 54.5 percent to 45.5 percent.
Faulconer will replace Bob Filner, who resigned after a wave of sexual harassment allegations. Filner was San Diego's first Democratic leader in 20 years.
Faulconer said on Wednesday that he will continue voter-approved fiscal measures like cutting pensions for city workers and putting city services up for private bidding. As he did throughout the campaign, he played down his party affiliation in an increasingly Democratic city.
Though Faulconer, 47, and Alvarez, 33, held sharp ideological differences, they 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, 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.
The new mayoral post 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 Associated Press contributed to this report.