A fourth boy was released, after the court ruled there was insufficient evidence to bring charges.
All four boys are aged sixteen.
Prosecutors in the high profile case had sought murder charges on all four youths, after their alleged victim was repeatedly kicked in the head following a party in central Stockholm.
The boy later died of his injuries.
Although street violence remains comparatively rare in Sweden, the case has sparked intense interest here.
Two boys, also present at the party where the attack took place, have formed a movement named ”Protect us from Street Violence”, which has attracted some 34,000 members via the Internet.
The two are hoping thousands will turn out for a demonstration against youth violence due to be held in central Stockholm on Friday.