In March, Pinch issued a warrant for Yunus's arrest after he refused to come to Australia to give evidence in the case.
Yunus, who was information minister in the cabinet of former president B.J. Habibie, has called his accusers liars.
Another former Indonesian army officer whom the coroner said took part in the killings, Christoforus da Silva, is thought to be living in retirement on Flores island.
Murdani, who was armed forces chief between 1983 and 1988, died three years ago.
TENSION
The deaths of the Balibo five -- Greg Shackleton, Tony Stewart, Gary Cunningham, Brian Peters and Malcolm Rennie -- have been a long-running source of tension between Australia and Indonesia, with relatives accusing both countries of a cover-up.
Pinch said she would now ask the Australian government to consider pursuing war crimes charges against those involved.
Her finding ends a 30-year campaign by relatives of the dead journalists and cameramen, who believed the men were deliberately killed.
"Proper respect has now been paid to these Australian citizens who have been brushed aside," Shackleton's widow Shirley told reporters outside the court.
Pinch ruled there was no evidence to support claims the Australian government had advance notice of Indonesia's plan to invade East Timor after the withdrawal of the territory's former Portuguese rulers.
The invasion led to 24 years of Indonesian control of East Timor, a country of about 920,000 people which voted in 1999 to break free of Indonesian rule and which gained full independence in 2002.
Pinch also recommended that Australian and Indonesian authorities work together to find the remains of the five men and return them to Australia for burial.
(Additional reporting by Ahmad Pathoni in Jakarta; Editing by Roger Crabb)
