Elphbert Laforteza also faces felony charges of possession of ingredients to make a destructive device and possession of a destructive device in a public place.
The defendant, who graduated last week but didn't walk with his class, faces up to six years in state prison if convicted, said Deputy District Attorney Mary Loeb.
Laforteza's arraignment at the South Bay Courthouse was attended by a large group of supporters, many of whom wore T-shirts printed with the words, "We love and support Elphbert."
Defense attorney Daniel Smith said prosecutors are "making an example" of his client.
"Elphbert is very remorseful and continues to offer advice to other seniors that pranks are not what they used to be," Smith said after the hearing. "It's unfortunate that it has risen to the level of criminal charges. We would have rather it stayed in the education system."
Smith said his client has suffered enough already, including the loss of a scholarship.
Judge H. Ronald Domnitz allowed Laforteza to remain free on supervised release, meaning the defendant must stay 100 yards away from any school unless he is attending higher education classes.
The defendant also is required to check in with court officials on a regular basis; cannot leave San Diego County without permission; is subject unannounced searches by police; and must abide by an 8 p.m.-6 a.m. curfew.
"Sorry if you're dating someone," the judge told the defendant, who remained somber during the court proceeding.
Some of Laforteza's former classmates, including Julissa Muniz, spoke out in support of him.
"They're blowing everything out of proportion," Muniz said. "He's super smart and super caring. If he thought for one second that it would hurt someone, he never would have done it."
Smith said he wouldn't even classify the device in question as a "bomb."
"It's more like a popper, like the kind you would use on New Year's Eve," the attorney said outside court.
Prosecutors declined to comment on the device involved.
On June 5, five crude homemade chemical bombs exploded in trash barrel during the lunch hour at San Ysidro High.
Three others were disabled by the bomb squad and officers found four other devices partially assembled in Laforteza's backpack, authorities said.
Nobody was injured and no property was damaged in the explosions.
Laforteza told investigators he had brought a dozen of the bottle bombs to the Airway Road campus, according to Maurice Luque, a spokesman for the San Diego Fire-Rescue Department.
Principal Hector Espinoza called it a "very bad prank."
Laforteza -- an all-league football player and an ROTC cadet -- applied but was not admitted to the Air Force Academy, according to a spokesman for the Air Force.
The defendant will be back in court July 13 for a readiness conference and Aug. 10 for a preliminary hearing.