Officers broke windows, pounded on the roof and shouted for the man they thought was there to surrender but he wasn't found there.
They then raced to another house about two blocks away, positioning an armored truck and robots outside. But he wasn't there either and the manhunt was still on Friday afternoon.
It is with a very sad heart that we announce the death of one of our Officers tonight. Pray for his family pic.twitter.com/3l9PXa1vuW— San Diego Police (@SanDiegoPD) July 29, 2016
Police Chief Shelley Zimmerman identified the dead officer as Jonathan DeGuzman, a 16-year veteran of the force who was married with two children. He suffered multiple gunshot wounds.
Officer Wade Irwin, 32, underwent surgery after being shot and was expected to survive, Zimmerman said. His wife was at the hospital during surgery.
Both officers were wearing bulletproof vests and body cameras, and quickly called for assistance from other officers, Zimmerman said.
Police initially said the shootout started following a traffic stop, but Zimmerman later clarified that detectives were trying to determine whether it was a traffic stop or an attempt by the officers to check out a pedestrian.
"It happened extremely quickly, very quickly," she said. "From the information that was put out that a stop was being made to that the officers called for emergency cover to when the other officers arrived on scene, we're talking very, very quickly, Seconds to a minute or so. Very quickly."
The male suspect was captured in a nearby ravine and was being treated Friday at a hospital. Police did not identify him but Zimmerman said he was in critical condition with a gunshot wound.
Residents were ordered to stay in their homes throughout the night as San Diego police and officers from other law enforcement agencies scoured ravines, yards, streets and alleys for other possible suspects. A helicopter hovered over the neighborhood.
About nine hours after the shootout, heavily armed police officers surrounded a house about a half-mile away, one of them using a bullhorn to urge a man to surrender. Authorities also detonated several devices at the scene that made deafening booms.
Zimmerman said a potential second suspect was holed up in the house and that information she did not describe led officers to the home.
A series of loud bangs have been heard at the SD SWAT location. Possibly flash bang grenades or pepper spray rounds. pic.twitter.com/NxyRpA0xkA— John Gregory (@abc7johngregory) July 29, 2016
She told reporters she had worked with Zimmerman before she was promoted to the police chief post in 2014.
"I can tell you he is a loving, caring husband, father. Talked about his family all the time," Zimmerman said. "I know him, and this is gut-wrenching. He cared. He came to work every day wanting to just make a positive difference in the lives of our community."
After visiting Irwin later at UC San Diego Medical Center, Zimmerman told reporters that the officer's prospects for recovery were good.
"It's a little bit of a long haul until he makes a full recovery, but the good news is that he is going to survive and he is going to recover," she said outside the hospital.
The shooting came as law officers around the country are on high alert following the killing of officers in Dallas and Baton Rouge, Louisiana, this month.
"Violence against the men and women who wear the badge is violence against us all," San Diego Mayor Kevin Faulconer said after the shootings in his city. "I ask all San Diegans and all people across our nation to join together in support of our officers who courageously protect our communities. We need them and they need us."
U.S. Attorney General Loretta Lynch mentioned the San Diego shooting during a meeting Friday with police officers and other first responders in Baton Rouge, where a gunman killed three on-duty law enforcement officers earlier this month.
"I know this community, more than most knows exactly what these families are feeling at this moment," she said.