President Donald Trump and other elected officials decried the attack which comes exactly six months since 11 people were killed at a Pittsburgh synagogue in the deadliest assault on Jews in US history.
An off-duty Border Patrol agent working as a security guard at the Chabad of Poway fired at the shooter as he fled, missing him but striking his getaway vehicle, San Diego County Sheriff William Gore said.
The gunman, identified as John Earnest, 19, used an AR-type assault weapon, Mr Gore said. There were indications that the gun might have malfunctioned after firing numerous rounds inside the synagogue, the sheriff said.
Shortly after fleeing, Earnest called police to report the shooting, San Diego Police Chief David Nisleit said.
When an officer reached the man, “the suspect pulled over, jumped out of his car with his hands up and was immediately taken into custody,” Mr Nisleit said.
A girl and two men were wounded as the Jewish congregation gathered for Passover, a weeklong commemoration of the deliverance of the ancient Hebrews from slavery in Egypt.
The three were in stable condition, authorities said.
A Jewish leader in the San Diego area identified the victims of the shooting.
Lori Kaye, 60, of Poway was killed, Rabbi Yonah Fradkin, executive director of Chabad of San Diego County, said in a statement.
Those injured in the shooting on Saturday were Rabbi Yisroel Goldstein, Noya Dahan, eight, and Almog Peretz, 34, he said.
“In the face of senseless hate we commit to live proudly as Jews in this glorious country,” he added.
“We strongly believe that love is exponentially more powerful than hate. We are deeply shaken by the loss of a true woman of valour, Lori Kaye, who lost her life solely for living as a Jew.”
Earnest has no criminal record, but investigators were looking into a claim he made in an online manifesto about setting a fire at a mosque in nearby Escondido last month, Mr Gore said. There was damage but no injuries.
Mr Gore said authorities were reviewing copies of his social media posts and were investigating the attack as a possible hate crime.
While no motive for the attack has been confirmed, the San Diego county sheriff, William Gore, said investigators were reviewing social media posts and an “open letter” published before the attack.
Posted to online forum 8chan and littered with antisemitic and racist language, the document was similar to one published on the same website by the suspect arrested after the mass shooting inside two mosques in Christchurch, New Zealand last month.
The document’s author, who identified himself as John Earnest, claimed to have been motivated by the Christchurch massacre and another shooting at Pittsburgh’s Tree of Life synagogue in which a white supremacist killed 11 people.
There was no known threat after Earnest was arrested, but authorities boosted patrols at places of worship as a precaution, police said.
Minoo Anvari, a member of the synagogue, told media outlets that her husband was inside during the shooting. She said he called to tell her the shooter was shouting and cursing.
She called the shooting “unbelievable” in a peaceful and tight-knit community.
“We are strong; you can’t break us,” Ms Anvari said.
Donny Phonea, who lives across the street from the synagogue, turned off his power drill and heard someone shout, “Police!” Then he heard three or four shots.
The 38-year-old bank auditor looked over his fence facing the synagogue and saw people hiding behind an electrical box in the car park of a neighbouring church.
At that point, he knew something was “very, very wrong”, went inside and closed his doors and garage.
“I’m a little taken aback,” said Mr Phonea, who moved to Poway two weeks ago. “I moved here because safety was a factor. Poway is very safe.”
Mr Trump offered his sympathies on Saturday, saying the shooting “looked like a hate crime” and calling it “hard to believe”.
“Our entire nation mourns the loss of life, prays for the wounded and stands in solidary with the Jewish community,” Mr Trump said later at a rally in Wisconsin.
“We forcefully condemn the evils of anti-Semitism and hate, which must be defeated.”
The mayor of Poway, who tweeted that he got a call from the president offering help, also denounced what he called a hate crime.
“I want you know this is not Poway,” Mayor Steve Vaus said.
“We always walk with our arms around each other and we will walk through this tragedy with our arms around each other.”
Democratic Governor Gavin Newsom said he joins the community in grief.
“No one should have to fear going to their place of worship, and no one should be targeted for practising the tenets of their faith,” he said.
Residents of Pittsburgh gathered at the Tree of Life synagogue for a vigil in the wake of the shooting.
Pittsburgh mayor Bill Peduto tweeted a picture of the gathering of over 100 people in a steady rain.
It was accompanied by text that read: “We gather. Again. Always. Until we drive hate speech & acts of hate out of our city, our state, our nation, our world.”
The Tree of Life released a statement, saying “We know first-hand the fear, anguish and healing process such an atrocity causes, and our hearts are with the afflicted San Diego families and their congregation.”
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