The list included all 40 commanders jailed in connection with the "Ergenekon" and "Sledgehammer" trials involving hundreds of defendants accused of trying to bring down the government.
The decision marked a departure from last year's tumultuous YAS when the top four commanders quit before the meeting even began to protest the jailing of hundreds of officers, including 20 percent of the military's generals.
YAS, which Prime Minister Recep Tayyip Erdoğan chairs, meets twice yearly to decide key military promotions. The council also promoted 29 generals and admirals to higher ranks and extended the tenure of 33 others, the Turkish Armed Forces website said.