The downing of the aircraft, at a point close to the sea borders of both countries, provided a demonstration of Syria's formidable Russian-supplied air defenses; one of the many reasons for Western qualms about any military intervention to halt bloodshed in the country.
Ankara's once-friendly relations with Damascus had already turned icy over President Bashar al-Assad's violent crackdown on a 16-month-old revolt, but signals from both sides suggested neither wanted a military confrontation over the incident.
"It is not possible to cover over a thing like this, whatever is necessary will be done," Turkish President Abdullah Gül said, according to state news agency Anatolia, adding that Ankara had been in telephone contact with Syrian authorities.
He said it was routine for fast-flying jets to cross borders for a short distance and that an investigation would determine whether the F-4 fighter was brought down in Turkish airspace.
Syria's military said the Turkish aircraft was flying low, just one kilometer off the Syrian coast, when it was shot down.
"The navies of the two countries have established contact. Syrian naval vessels are participating along with the Turkish side in the search operation for the missing pilots," it said.
With the second biggest army in NATO, a force hardened by nearly 30 years of fighting with the terrorist Kurdistan Workers' Party (PKK), Turkey would be a formidable foe for a Syrian military already struggling to put down a popular uprising and an increasingly potent insurgency.
Turkish Prime Minister Recep Tayyip Erdoğan chaired an emergency security meeting on Friday evening after which his office said it is "understood" that Syria had downed the plane and confirmed that both sides were searching for the two missing airmen.
"Turkey will present its final stance after the incident has been fully brought to light and decisively take the necessary steps," said a statement from Erdoğan's office.
Turkish newspapers were less restrained.
"They (the Syrians) will pay the price," said Vatan, while Hürriyet daily said "He (Assad) is playing with fire."
The joint Turkish-Syrian search and rescue operation sits uneasily with Turkey's hosting of the rebel Free Syrian Army fighting to topple Assad, once a personal friend of Erdoğan.
The souring of relations over the past year has provoked concern among Turks that Syria may revive its former support for the PKK in southeastern Turkey.
"It's possible the Turks were sending jets in the area in response to an apparent escalation of the PKK's activities," Hilal Khashan, political science professor at the American University of Beirut, told Reuters.
"Turkey may suspect that Syria and Iran are supporting Kurdish rebel activities now as a reaction to Turkish support of the Syrian revolt," he said.
However, Khashan said he did not expect a harsh military reaction from Turkey. "It is under a tight leash by the United States. They don't want to start a war tomorrow."
A civil war, or something closely resembling one, is already in full swing in Syria, where fighting or shelling engulfed parts of the cities of Aleppo, Hama, Homs, Deir al-Zor and Douma, according to the Syrian Observatory for Human Rights.
The British-based watchdog also reported fierce clashes and shelling in the town of al-Bab in Aleppo province, where army helicopters were flying overhead. It said rockets and gunfire had killed three people in al-Qusair, a town in Homs province. Two men were killed in an ambush by security forces in Hama.
Turkey fears the fighting, much of which pits majority Sunni Muslim dissidents and rebels against Assad's Alawite-dominated security forces, could unleash a flood of refugees over its own border and ignite regional sectarian conflict.
It already hosts 32,000 Syrian refugees near the border. The opposition Syrian National Council meets in Istanbul.
Ankara has previously floated the possibility of setting up some kind of safe haven or humanitarian corridor inside Syria, which would entail military intervention, but has said it would undertake no such action without U.N. Security Council approval.
Turkey has said however that Assad must go.
It was unclear why the Syrians had shot down the aircraft, which, having left a base in Malatya, was flying close to a corridor linking Turkey with Turkish forces on Turkish Cyprus.
"The Syrian military may have taken a calculated gamble by downing the Turkish plane, which could boost the morale of Assad's loyalists after increased defections from the military," said Yasser Saadeldine, an opposition Syrian commentator.
"A Turkish retaliation would fit into the fantasy he (Assad) is peddling that the uprising is a foreign conspiracy."
Russia and China, Assad's strongest backers abroad, have fiercely opposed any outside interference in the Syrian crisis, saying envoy Kofi Annan's peace plan is the only way forward.
Russian Foreign Minister Sergei Lavrov said after talks with his Syrian counterpart on Friday that he had urged Syria to "do a lot more" to implement Annan's UN-backed proposals, but that foreign countries must also press rebels to stop the violence.
Lavrov said the Syrian authorities were ready to withdraw troops from cities "simultaneously" with rebels. A Syrian military pullback and a ceasefire were key elements in Annan's six-point peace plan, most of which remains a dead letter.