The incident rocked the Balkan nation, which has not seen a school shooting of this magnitude for decades and where one cabinet minister called it the "biggest tragedy" to occur in the Serbian school system in recent history.
"Eight children and a security guard were killed, while six children and one schoolteacher were wounded," the interior ministry said.
Belgrade police chief Veselin Milic identified the dead students as seven girls and one boy, born between 2009 and 2011.
The shooting occurred at 8:40 am (0640 GMT) at an elementary school in Belgrade's downtown Vracar district. Serbian elementary schools go up to eighth grade, educating children aged seven to 15.
Police moved quickly to seal off the neighbourhood as parents rushed to the scene, where students were visibly distraught as they waited outside the school.
Milan Nedeljkovic, president of the Vracar district, said the school's security guard likely prevented more deaths by putting himself in the line of fire.
The guard "wanted to prevent the tragedy and he was the first victim", Nedeljkovic told reporters outside the school.
"Probably the tragedy would be even bigger if the man did not stand in front of the boy who was shooting," he added.
Authorities later identified the suspect as Kosta Kecmanovic, a 13-year-old student, saying that he was armed with two pistols, one in his backpack and one that he used.
The suspect "planned the shooting for a month and made a list of kids he planned to kill," Milic told a press conference.
"The sketch looks like something from a video game or a horror movie, which indicates that he planned in detail, by classes, whom to liquidate," he added.
Interior Minister Bratislav Gasic said the suspect's father, who owned the alleged weapons used in the shooting spree, was also under arrest.
"The father claims that the arms were locked in a safe with a code, but apparently the kid had the code, as he managed to take the pistols and three magazines with 15 bullets each," said Gasic.
Hours after the incident, officials said an array of resources were being deployed to assist students, families and faculty connected to the shooting.
"A team of psychologists and others... were immediately called to provide adequate support to students, employees and parents during this traumatic period," Education Minister Branko Ruzic told media.
Ruzic went on to call the shooting the "biggest tragedy" that has occurred in the Serbian school system in recent history.
"It is unimaginable when you see those scenes, what it was like for those children who felt that fear, for the guards and teachers when they tried to protect the children," Ruzic added.
The minister dismissed media reports that bullying was a possible motive in the shooting, saying "no conclusions" had been reached.
Serbia will observe three days of mourning, Ruzic added, while a minute of silence will be observed in schools across the country on Thursday.
'Serious Gunshot Wounds'
The head of Belgrade's main hospital KCS, Milika Asanin, said doctors were operating on several of the wounded.
"One male student is in a serious condition with serious gunshot wounds to the chest and neck, and the other male student was injured in his lower leg," Asanin told Serbian news outlet RTS.
"The girl student was wounded in the stomach and both arms, and the teacher in the stomach and both hands," he said.
Schools across Belgrade were closed following the shooting, according to state media, as shock spread through the capital.
Astrid Merlini, whose daughter was in the school during the shooting, said teachers moved quickly to hide students as the attack unfolded.
"When (my daughter) saw the security guard fall, she immediately rushed back to class. She was scared. She told her teacher, there is a shooting upstairs," Merlini told AFP.
"The teacher immediately sheltered the children, locked them in the class."
Gun violence in schools is extremely rare in Serbia, where purchasing a firearm requires a special permit.
Following the shooting, EU foreign policy chief Josep Borrell offered "deep condolences to the families and close ones of the victims".