Bilbray issued a written statement thanking his supporters in the high-priced campaign and said it was time to put the partisan nature of the race behind them.
"While Scott and I differed sharply on how to handle the issues facing our nation, now is the time to put those differences aside and find common ground to address our country's many challenges," the statement said.
Bilbray spent six full terms and one partial term in the House. He promoted environmental protection and alternative energy. He led the legal fight to preserve a memorial cross on top of San Diego's Mount Soledad.
Bilbray trailed Peters by nearly 3,900 votes when he threw in the towel, UT San Diego said. There were 120,000 uncounted ballots left in San Diego County but it was unclear how many came from the 52nd District.
The district's boundaries were redrawn for the 2012 election cycle and stretched from downtown San Diego north to Poway and La Jolla. Republicans maintained a 2-percent advantage in registered voters, UT San Diego said, but outside political action committees pumped $5.6 million into the closely contested race.
Peters, a former San Diego City Council member, was in Washington Friday to take part in freshman orientation for newly elected House Democrats. Bilbray was in the capital for the lame-duck session.