The formation of the council is the latest step in ending years of mistrust over Turkish accusations of Syrian support for the separatist Kurdistan Workers' Party (PKK).
Ten years ago tensions between the two countries over the issue led to increased troop deployments along their shared border.
Following Tuesday's meeting, Walidal-Muallem, Syria's foreign minister, said that Damascus regarded the PKK as a "terrorist organisation banned" in his country.
Military relations between Syrian and Turkey developed for the first time earlier this year, causing Israeli media to question arms sales to Turkey, a Nato member.
As Turkish-Syrian relations have improved, Turkish-Israeli ties have deteriorated sharply.
Relations became strained over Recep Tayyip Erdogan's, Turkey's prime minister, harsh criticism of Israel's three-week offensive in the Hamas-ruled Gaza Strip in December and January.
Both Turkey and Israel have denied the cancellation of the air force exercises, scheduled for this week, posed any threat to their long-standing bilateral ties and strategic interests.
Al-Muallem commended Ankara's cancelling of the exercises.
Al-Muallem said: "We extremely welcome that decision. This decision is based on Turkey's approach towards Israel and reflects the way Turkey regards the Israeli attack in Gaza."
On Tuesday, the US state department objected to Turkey's last-minute decision to exclude Israel from the exercise.
"We think it's inappropriate for any nation to be removed from an exercise like this at the last minute," said PJ Crowley, a state department spokesman.
Turkey has denied any political motive behind the decision to "postpone" the exercise with Israel and called on Israel to display "common sense" in their statements.
Addressing journalists in Aleppo, Ahmet Davutoglu, Turkey's foreign minister, said: "Our sensitivity on Gaza, East Jerusalem and al-Aqsa mosque are there.
"If these sensitivities are taken into consideration the peace process would resume in the region."
European Union candidate Turkey, under Erdogan's AK party, has deepened its ties and influence in the Middle East, expanding Ankara's foreign policy beyond its traditional Western-oriented focus and strengthening ties with countries such as Syria and Iran.
Israel, which has enjoyed close military co-operation with Turkey as well as bilateral trade worth nearly $3bn, has urged Ankara to consider cooling ties with Hamas and Iran, with Erdogan set to visit Tehran later this month.
Meanwhile, delegations from Syria, Turkey, Iran, Egypt, Iraq, Saudi Arabia, Kuwait, Jordan, Bahrain as well as representatives of the Organisation of Islamic Conference, the United Nations and the Arab League are holding a security conference in Sharm el Sheikh on Wednesday.
The sixth conference of Iraq's neighbouring states will discuss Iraq's security, border co-operation among the country's neighbours, preventing cross-border activities of terrorists and the smuggling of weapons into Iraq.