"For the future, we will really leave the arena of practical politics and we will focus ourselves especially on the matter of defence," said General Endriartono Sutarto on Sunday.
The annual meeting of the People's Consultative Assembly (MPR), which ends later on Sunday, will be the last in which unelected seats are reserved for the military and police.
Under democratic reforms agreed to in 1999, the military and police lose their 38 appointed representatives in both parliament and the MPR.
The new parliament which was chosen in April polls will be an all-elected body.
Susilo is set to become the
country's new president
The next MPR will be formed from the parliament and a new elected body called the Regional Representatives Council, and will hold its first meeting on 1 October.
The move marks the culmination of democratic reforms which began after the resignation of military-backed leader Suharto in 1998.
This year Indonesians directly elected their president after decades of the MPR picking the leader.
With more than half the votes counted, former general Susilo Bambang Yudhoyono, who is set to become Indonesia's president next month, is leading with 60.9% to Megawati Sukarnoputri's 39.1%.
Official results will be announced on 5 October.
Endriartono had pledged to keep the military neutral in elections this year and ordered them not to vote in the parliamentary and presidential polls.
He said soldiers would only vote in 2009 if the political situation was conducive.
"If the political life is already good, democratic life is proceeding healthily and there are no political forces trying to persuade TNI [the armed forces] to support them, then soldiers will have their voting rights and can vote in 2009," he said.
He called on legislators elected on 5 April to create a professional military.
"If they really feel that this state needs a professional and strong force, strong in its duties and functions, then they should of course fight for the armed forces to really become a professional force," Endriartono said.