"I feel wonderful. I believe that justice will be fulfilled because I am completely innocent," Mr Filipovic said following his release.
The military court ruled that there had been "major violations" of criminal procedure when Mr Filipovic was sentenced to seven years imprisonment in July.
Mr Filipovic, 49, was named "European Internet Journalist of the Year" at the annual NetMedia awards in London earlier this year, and was regarded as a prisoner of conscience by the human rights pressure group, Amnesty International.
New trial
The case against him centred on articles written about alleged atrocities committed by Yugoslav troops in Kosovo last year, for the website of the London-based Institute of War and Peace Reporting (IWPR).
"I feel wonderful. I believe that justice will be fulfilled because I am completely innocent," Mr Filipovic said following his release.
"I believed in the military judiciary and that this strange ruling was untenable. And I believe that everything will end the only way it is possible, I simply am not guilty."
He thanked those who had campaigned for his release and said he hoped all other political prisoners would be freed.
The state news agency, Tanjug, said a new trial had been ordered.
Crackdown
At his trial by a military court in the southern city of Nis, Mr Filipovic denied charges of spying and "spreading false information", but the court ruled that he had gathered confidential military information for foreign organisations.
His reports included testimony from a Yugoslav army commander who admitted that he watched as a soldier decapitated a three-year-old ethnic Albanian boy in front of his family.
Another report described how tanks in the commander's unit indiscriminately shelled a Kosovo Albanian village before paramilitary police moved in and massacred the survivors.
His conviction was widely interpreted as an attempt to crack down on the independent media as well as on reformist elements within the Yugoslav Army, some of whom had provided him with information.
Health concerns
"He suffered a potentially life-threatening heart condition, as well as a dramatic loss of weight, with the authorities denying him essential medical care," the IWPR said.
The organisation's executive director, Anthony Borden, added: "Filipovic was one of the first to signal the cracks within the military establishment itself, which would become decisive during the sudden revolution in Serbia.
"In that sense he served as a crucial protagonist in the changes."
Apart from the IWPR, Mr Filipovic also worked for the independent Belgrade daily newspaper Danas, and the French news agency AFP, reporting from the southern city of Kraljevo.