Turkey decided to reroute planes because it considers Syrian airspace unsafe, CNN reported. Passengers traveling to Saudi Arabia will be most affected.
Planes, which used to fly to Jeddah over Aleppo and Hatay Kamisli, will use airspace belonging to Jordan and the Turkish Republic of Northern Cyprus.
Meanwhile, Russian President Vladimir Putin canceled a trip to Turkey after Ankara forced down a passenger jet that originated in Moscow it alleged carried military equipment and ammunition destined for the embattled Syrian regime.
Turkish Prime Minister Recep Tayyip Erdogan denied the cancellation of a trip set for Sunday was related to Wednesday's grounding of a Syrian Air A-320 Airbus jetliner with 35 passengers en route to Damascus.
A Putin spokesman told the Interfax news agency the visit could be rescheduled for Dec. 3.
Erdogan visited Moscow in June to discuss the Syrian crisis.
Moscow expressed dismay at Turkey's actions, with the Foreign Ministry saying in a statement the landing -- forced by two Turkish F-16 warplanes because Turkish officials suspected the jet's cargo contained weapons and ammunition -- had "threatened the life and safety" of 17 Russian citizens aboard.
It said Moscow "continues to insist on an explanation of the reasons for these actions by the Turkish authorities."
Syria accused Turkish officials assaulting the crew. It also denied any illegal cargo was on board and demanded the return of whatever had been seized. Turkish officials said they might confiscate the material.
The official Syrian Arab News Agency quoted a Foreign Ministry statement as saying Turkish officials forced the plane to sit unattended on the tarmac at Esenboga International Airport in Ankara, the capital, for hours, leaving the occupants to wonder why they were there.
After passengers were escorted into a waiting lounge, "Turkish security authorities subjected the plane to search and assaulted the plane crew," the ministry said. The plane and passengers were allowed to leave early Thursday.
Turkish Foreign Minister Ahmet Davutoglu said it was "unacceptable" for Turkish airspace to be used for weapons transfers to the regime of President Bashar Assad, which Turkey fervently opposes.
"We are determined to control weapons transfers to a regime that carries out such brutal massacres against civilians," Davutoglu said in remarks shown live on Turkish television.
Erdogan said at a news conference the cargo included unspecified "munitions" from a Russian "institution equivalent to our Mechanical and Chemical Industry Corp.," referring to the state-run manufacturer that supplies Turkey's military.
The munitions included "military tools, equipment and ammunition to the Syrian Defense Ministry," he said.
An unidentified senior Russian official told Interfax, "No weapons, systems or other kinds of military equipment was on board the passenger aircraft, nor could there be."
He said Russia would never carry out military sales to Syria illegally, "especially with the use of civilians."