With 100 percent of the precincts reporting, Faulconer received 137,296 votes, or 54.53 percent, versus Democrat David Alvarez, who received 114, 478 votes, or 45.47 percent in Tuesday's special election, the San Diego County election office reported on its website.
Before all the votes were tallied, Faulconer, a city council member, told supporters Tuesday he "can't wait to be the next mayor of this fabulous and great city," the Los Angeles Times reported.
"This city has gone through a lot in the last year, but we knew that as San Diegans we were better than that," Faulconer said.
Faulconer will complete the 33 months remaining in Filner's term. He will be sworn in March 3.
Faulconer praised Acting Mayor Todd Gloria, a Democrat who endorsed council member Alvarez, for "getting this city back on track" after Filner resigned Aug. 31 following months of controversy, the Times said.
Filner, elected San Diego's mayor after 20 years in Congress, was the city's first Democratic leader since since 1992 but served less than a year.
"America's 8th largest city is back in Republican hands," tweeted Republican leader Tony Krvaric Tuesday as Faulconer maintained his lead over Alvarez.
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