Pollycarpus Priyanto, a former Garuda Indonesia pilot, is serving a 20-year jail term after he was convicted of poisoning Thalib in January last year.
Intelligence chief acquitted
Major General Muchdi Purwoprandjono, a former deputy chief of the State Intelligence Agency, was also prosecuted on charges of plotting the killing.
Purwoprandjono was acquitted by a different court, although lawyers have appealed against the ruling.
The high-profile trial is viewed as a test of how far the southeast Asian country judicial system has progressed since introducing civilian rule in 1998.
Indonesia was ruled by a military government for 32 years until the death of President Suharto paved the way for democratic elections.
However, the country is struggling to build an independent judiciary and Thalib had exposed a string of incidents involving military abuse during Suharto’s time in power.
A 2005 presidential fact-finding investigation concluded that the state was most likely behind the killing, but its recommendations for a full inquiry were dismissed.