Erdoğan convened the Supreme Military Council
) as scheduled on Monday despite the presence of only nine of the 14 generals who would normally attend the twice-yearly meeting to decide key promotions in NATO's second largest armed force.
The meeting will run for four days.
Long-running strains between the secularist military and the ruling conservative AK Party, which has Islamist roots, boiled over on Friday when Chief of General Staff Işık Koşaner resigned, along with the army, navy and air force commanders, in protest at the arrest of fellow officers.
The fifth general missing from Monday's meeting was one of some 250 officers now jailed on charges linked to various alleged anti-government plots dating back to 2003.
The resignations will enable Erdoğan to consolidate control over a once-omnipotent military that has staged three coups since 1960 but whose power has been curbed by European Union-backed reforms since pushing an Islamist-led government out of power in 1997.
"The transition from the old guard in the military high command to the new will be relatively smooth," said Royal Bank of Scotland analyst Timothy Ash.
At the heart of the matter is the alleged "Sledgehammer" plot, based on events at a 2003 military seminar. Officers say evidence against them has been fabricated and that allegations of a coup plot arose from a mere war games exercise.
Chairing the YAŞ meeting, Erdoğan sat alone at the head of the table where normally he would sit beside the chief of staff. Defense Minister Ismet Yılmaz also attended.
Erdoğan has moved quickly to designate former gendarmerie chief General Necdet Özel as acting chief of staff, who has been portrayed positively as a constitutionalist in pro-government media. Özel is not expected to be confirmed as the overall commander until the key promotions are announced on Thursday.
Erdoğan did not take part in the YAŞ afternoon session and instead held direct talks with Özel. The prime minister then met the head of Turkey's intelligence agency and Interior Minister Idris Naim Sahin. No statements were made.
The council meeting will resume on Tuesday morning.
The prime minister joined the generals in a traditional visit to the mausoleum of soldier-statesman Mustafa Kemal Ataturk, founder of modern Turkey, on a hill in the capital.
The army has hitherto regarded itself as the guardian of Ataturk's secularist vision for a republic he established in 1923 out of the ashes of the Ottoman Empire.
After laying a wreath at Ataturk's tomb, Erdoğan wrote in the mausoleum visitors' book: "Our armed forces are making a major advance in their defense duties and through improving their vision."
President Abdullah Gül has denied that the resignations have triggered a crisis and financial markets shrugged off the resignations on Monday.
Erdoğan's regular address to the nation on Saturday focused on plans for a new constitution in the EU-candidate country, which is touted as a democratic model for a region cast in turmoil.
But the generals' protest over what they say is the unjust way the Sledgehammer case is being prosecuted has clouded the start of Erdoğan's third term in office.
His AK Party won 50 percent of the vote in a parliamentary election in June, and the dispute risks deepening a polarization in Turkish politics and society at a time when consensus is needed for proposed constitutional changes.
But the election result showed voters cared more about a booming economy than criticism that Erdoğan was amassing too much power.
Initial fears of a broader clash developing between the military and the government have receded, according to Ash.
"The consensus over the weekend is that the resignations mark the final end of the military's dominant position in Turkish society and finally show civilian control over the military has been established," he said.
However, analysts have express concerns about how the jailing of so many officers and disruption in the top ranks is affecting the military's operational ability as it faces a fresh wave of guerrilla violence.
In a reminder of that challenge, Kurdish guerrillas killed three soldiers in a clash in eastern Turkey on Monday.
Just how much control Erdoğan wants to exert at this stage should be clear once the promotions are known. The government opposes some leading candidates while others are on trial accused of trying to overthrow the government.
Among those at the YAŞ was Aegean Army commander General Nusret Taşdeler, whose attendance had been uncertain after prosecutors ordered his arrest last week along with 21 others over claims that the military set up anti-government websites.
This latest case was seen as one of the triggers behind the resignations of Koşaner and the other generals.
The most highly awaited issue is who will be appointed to head the land forces command.
Potential candidate General Saldiray Berk is likely to be ruled out as he faces trial related to "Ergenekon," an alleged secret network intent on undermining the AK party.
The commander of Turkey's military academies, General Bilgin Balanli, previously in line to take over the air force, is in jail.