Marcus Anthony Eriz, 24, has been charged with felony murder and discharge of a gun at an inhabited dwelling, with sentencing enhancements for causing death, county District Attorney Todd Spitzer said at an afternoon news conference.
Wynne Lee, 23, was charged with accessory after the fact and concealing a firearm in the vehicle.
Authorities believe Lee was the driver and Eriz was the gunman. The vehicle, a white Volkswagen, has been recovered, as has a weapon.
"In a civilized community, we should be able to drive our kid to school and not worry that they're going to be shot in the back," Orange County Supervisor Katrina Foley said at the press conference.
The two defendants, both residents of Costa Mesa, made a brief, virtual court appearance in Orange County on Tuesday.
A judge agreed with prosecutors' requests to increase Eriz's bail from $1 million to $2 million and set Lee's bail to $500,000.
Those bail amounts could be revisited when they return to court for an arraignment expected June 18.
Orange County DA discusses Aiden Leos case
Lee had initially been booked on murder charges, which prosecutors decided not to pursue against her in favor of the lesser charges. Spitzer said the charges reflect her alleged behavior after the shooting, rather than during the events leading up to the shooting, when she was believed to be driving the car.
"We all agreed that with respect to Ms. Lee, the evidence supported a filing of her behavior after the weapon was fired, but not with respect to conduct leading to that event," Spitzer said.
If convicted on all counts, Eriz faces a maximum sentence of 40 years to life, while Lee could be sentenced to three years in state prison and one year in county jail, according to the DA's office.
Spitzer on Tuesday emphasized that no other individuals were considered suspects in the case, and he asked for any harassment based on social media rumors to stop.
"They might be family members or whatever," the DA said. "I'm asking you to leave those people alone. ... They are not being looked at as criminals."
Aiden was buried Monday in a private ceremony.
White Volkswagen seized from Whittier home
The more than two-week manhunt came to an end Sunday with the arrest of Eriz and Lee at their home in Costa Mesa, according to the California Highway Patrol.
Aiden was killed May 21 while his mother was driving him to kindergarten. The boy was sitting in a booster seat on the right rear passenger side when someone in another vehicle opened fire between 7:55 and 8:15 a.m. on the northbound 55 Freeway between the 22 Freeway and Chapman Avenue.
Aiden was rushed to Children's Hospital of Orange County, where he was pronounced dead.
Authorities say there was a tremendous outpouring of support, and a flood of tips from the public on the case.
Officials have released few details about the circumstances that led to the suspects' capture. But they have previously said a man and a woman were driving a white Volkswagen, and it is believed the male passenger fired the shots that killed Aiden.
The investigation led them to a home in Whittier, where they found and seized a white Volkswagen matching the description of the suspects' vehicle.
Neighbors of the home say they believe Eriz's grandmother lives there.
"It's kind of insane knowing that somebody five houses down the street was involved in this heinous crime," said neighbor Dave Kampa.
Aiden Leos case: Corona auto body shop owners describe suspected shooter as former employee
Eriz's Instagram page displayed videos that show him shooting various types of firearms on a range.
A married couple that owns Platinum Collision, an auto body shop in Corona, described Eriz as a former employee who stopped working at the business in January.
"His Instagram page is false," said Tom Gregg, referring to the suspect's social media page that suggested he still worked at the shop.
Gregg and his wife, Stephanie Gregg, condemned the fatal shooting, which she described as "devastating," and expressed their condolences to Aiden's family. "To have any kind of link is just too much," Stephanie Gregg said.
They added that Eriz recently sent a text, just a week after the shooting, asking if there were any positions open at any of the company's locations, and saying he also knew an office manager looking for a position.
Community groups and local government agencies contributed to a reward fund that grew to at least $500,000 to find the suspects.
On Monday, CHP officials said they weren't prepared to discuss whether any reward money will be paid out after the arrest of the two suspects.
A poignant memorial service was held Saturday afternoon at Calvary Chapel Yorba Linda.
'Mommy, my tummy hurts': Aiden Leos' sister describes little brother's final moments
Joanna Cloonan, the boy's mother, eulogized her son in an emotional tribute. She opened her remarks by expressing gratitude for the outpouring of support from loved ones and strangers alike.
"Your kindness, your prayers, your support and unbelievable generosity has helped provide me with so much strength, so I may stand on my own two feet today, in front of you, and share the beauty of who Aiden was and still is," Cloonan said.
"The joy he brought into our lives was insurmountable," she said. "My heart melted every time he laughed."
In lieu of flowers, the family has requested that supporters make donations to assist the family through a pair of GoFundMe pages that can be found here and here.