Wednesday's conviction comes three weeks after a different court acquitted retired Major General Muchdi Purwoprandjono, the ex-deputy chief of the State Intelligence Agency, of plotting the murder.
That decision is being appealed by prosecutors.
Munir, who was a known critic of the country's military, died after consuming arsenic-laced orange juice on a Garuda Indonesia flight to Amsterdam in September 2004.
In 2005 a presidential fact-finding team concluded that the state was most likely behind the killing, but its recommendations for a deeper inquiry have been ignored.
The handling of the high-profile murder case has been seen as a gauge of progress in fighting corruption and upholding human rights in the young South-East Asian democracy of 235 million people.