A Hispanic man was later taken into custody, San Diego police chief Shelley Zimmerman told a news conference.
He was not immediately identified, but Zimmerman said he is now in the hospital in critical condition with a gunshot wound to the upper torso.
“We are still actively investigating the crime scene, including searching for any possible remaining suspects,” Zimmerman said.
“To have this happen to our police officers, we have seen this happen way too many times just in these last few weeks across our great country. It is tragic for everyone.”
The two officers radioed in that they were making a traffic stop late Thursday, then called for emergency backup soon after, she said.
Officers who arrived found the pair had been shot. Jonathan DeGuzman, 43, died in the hospital, Zimmerman said.
His wounded partner Wade Irwin came out of surgery later in the morning and is expected to survive, the police department tweeted.
The shooting took place around 11 pm Thursday (0600 GMT Friday) in the southeastern neighborhood of Southcrest, the San Diego Union Tribune reported.
It was too early to say whether the officers had been ambushed, Zimmerman said.
Police launched a manhunt after the incident. Zimmerman said an operation was carried out in which forces surrounded a house where a “potential second suspect may be inside.”
However, the San Diego Union Tribune later reported that no one was found.
The United States has been on edge for weeks following shootings of police officers in Dallas and Baton Rouge, Louisiana.
Those attacks followed anger among the black community over the shooting deaths of African-American suspects by white police in Minnesota and Louisiana.
Republican presidential candidate Donald Trump reacted on Twitter writing: “Two policeman just shot in San Diego, one dead. It is only getting worse. People want LAW AND ORDER!”
In her speech to accept the Democratic presidential nomination Thursday, Hillary Clinton highlighted the importance of easing race relations in the United States.