Thousands of supporters marched on the streets to welcome his release, singing and dancing in celebration.
The arrest of Bob Rugurika, director of the popular independent African Public Radio (RPA), sparked protests by civil rights activists and fellow journalists.
Rugurika was arrested on January 21 after broadcasting the purported confession of a man claiming he was one of the killers.
Lawyer Lambert Nigarura said he was released on a bail of 15 million Burundi francs ($9,500, €8,400), adding that while pleased he was out of jail there was a need for a proper investigation into the "real murderers of the three nuns."
For broadcasting the alleged confession, Rugurika was charged with complicity in the murders, "breach of public solidarity" and disclosing confidential information regarding a case.
The purported confession contradicted a police account of the crime and implicated the security services.
He faces up to 20 years in prison if convicted.
Burundi, a small landlocked nation in central Africa's Great Lakes region, emerged in 2006 from a brutal 13-year civil war. The political climate remains fractious ahead of local, parliamentary and presidential polls in May and June.
But the crowd of several thousand who turned out to celebrate Rugurika's release were peaceful.
"We are here for the return of the RPA director because we love him, we support him, his radio fights for freedom throughout Burundi," said one supporter, singing in the streets.
Opposition politicians and critics say the government is doing all it can to sideline political challengers ahead of the elections, including arrests, harassment and a clampdown on free speech.
The three Roman Catholic nuns, aged between 75 and 83, were murdered at a convent north of Bujumbura in September.