The outburst followed days of harrowing testimony from survivors of Norway's worst peacetime massacre.
The shoe missed Breivik but struck his co-defence lawyer, Vibeke Hein Baera, who was seated closest to the public gallery, during the presentation of an autopsy report.
Police said the attacker, who was quickly escorted from the court, was a brother of one of the 69 people Breivik methodically shot dead on the small island of Utoeya last July during a youth camp organised by the ruling Labour Party.
Breivik admits the killings but denies criminal responsibility, saying he was defending Norwegian ethnic purity from Muslim immigration and the multiculturalism policies of the governing Labour Party.
The Aftenposten newspaper named the man who threw the shoe as Hayder Mustafa Qasim, an Iraqi whose asylum seeker brother was killed on the island by Breivik.
"I took off my shoe, stood up, shouted at the killer, got eye contact with him and threw the shoe," Qasim told Aftenposten. "Go to hell killer! I shouted. He looked right into my eyes. I felt that he had understood my message."
"My brother was killed on Utoeya. He was alone in Norway, without family. The killer took his life. And he ruined my life and my family's life."
The incident evoked the gesture by an Iraqi reporter who hurled his shoes at former U.S. President George W. Bush in 2008. Hitting someone with a shoe is considered particularly insulting in the Middle East because footwear is regarded as unclean.
Some in the courtroom applauded Qasim's gesture, some said "finally" and others started to cry. Police, removed him from the court and increased their presence to avoid further interruptions of the trial, which is expected to last 10 weeks.
Local media quoted Breivik, 33, as saying after the incident: "If anyone wants to throw something, you can throw it at me when I'm entering or leaving the court.
"Don't throw things at my lawyers."
Friday's outburst was the first interruption of proceedings. Many observers have been surprised by the cool Nordic civility on display in the courtroom despite a killing spree which traumatised this nation of five million.
The incident came at the end of a week of harrowing testimony from survivors of Breivik's killing spree. As well as those shot dead, eight others died in a massive car bomb Breivik detonated outside the prime minister's offices in central Oslo.
Police played down the shoe throwing incident.
"We regard this as a spontaneous emotional outburst," Rune Bjoersvik, the police officer charge of police operations in the court, told Reuters.
"We wish it hadn't happened, but we don't regard this a dramatic breach of safety."
Throughout his trial Breivik has listened calmly to the descriptions of his killings and shown little emotion, except when hearing descriptions about how he was said to have let out "cries of joy" and laughed while shooting, which he has denied.
During Friday's hearing Breivik said one person at Utoeya had thrown an object at his face as he went about the small island shooting his victims. But he gave no more details.
Breivik has said he should either be executed or acquitted, calling the prospect of a prison sentence "pathetic" and an insanity ruling "worse than death". Ahead of his trial, court-appointed psychiatrists concluded he was psychotic but a second team came to the opposite conclusion.
If deemed sane, Breivik faces a 21-year jail sentence with indefinite extensions for as long as he is considered dangerous.
