Democrat Juan Vargas was the top vote-getter and Republican Michael Crimmins placed second in the race for the 51st Congressional District.
Vargas, a Democrat, wons with 45.7 percent of the vote followed by Republican Crimmins' 20.3 percent.
That second spot had been expected to go to former state Sen. Denise Moreno-Ducheny, D-San Diego, who instead finished third.
Under California's new "top-two'' primary system, the pair of candidates with the most votes will square off in the general election in the House races. The system also means means Democrats can vote for Republicans and Republicans can vote for Democrats.
Four other candidates split the rest of the vote in a district that has sent Rep. Bob Filner, D-San Diego, to the nation's capital for two decades -- often by wide margins. Filner gave up his seat to run for mayor of San Diego.