All were expected to make a full recovery. Two more children were grazed by bullets.
Police didn't disclose what led to the shooting, but said in a statement that the evidence "suggests that this was an isolated incident, involving the negligent discharge of a firearm, where innocent children and a staff member were unfortunately injured".
Authorities did not immediately identify a possible motive, saying the investigation was in its early stages.
Dr Aaron Strumwasser, at Los Angeles County-USC Medical Center, said: "I think he will do fine..."
The girl wounded in the wrist also remained hospitalized but was described as resting comfortably.
Three other people had minor face or head injuries, some from broken glass, but weren't shot, officials said. But the two children actually had grazing gunshot wounds, Strumwasser said. They've since been treated and released from the hospital.
Jordan said he saw a hole in the backpack, which the girl was holding, when she asked him to hide the gun for her.
The 12-year-old girl was reportedly taken to Los Angeles County's Juvenile Hall following the incident.
The sobbing girl told him: "I didn't mean to".
"I said 'No, '" he said.
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The school shares its campus with Belmont High School.
"We have our school mental health folks who are here to support the needs of the students and we will continue to work with those students", he said.
Parent Claudia Anzueto, 41, said her 12-year-old son was crying when he used someone else's cellphone to call her.
Anzueto said there were no metal detectors at the school.
But, he said, "she doesn't do bad things, she just stays quiet". "I fear for my son's life".
Castro has about 365 students in grades 6-8 and nearly all are Hispanic and many from low-income families.
Between 2000 and 2013, almost 17 per cent of 160 so-called active shooter incidents in the U.S. were in elementary, middle or high schools, according to a Federal Bureau of Investigation report.
Student Melanie Valencia, 13, said the school did a random security search Thursday, but that she's never been checked.
"We have a new culture here", Mitchell said at the time.