The reprisal, just weeks before the annual hajj when thousands of Turkish pilgrims head to the Muslim holy places in Saudi Arabia on a route that would normally take them through Syrian airspace, came despite a flurry of diplomacy on Saturday intended to calm soaring tensions between the neighbours.
Syria accuses Turkey of channeling arms from Gulf Arab states to rebels fighting its troops, who have been under mounting pressure across large swathes of the north, including second city Aleppo.
The flight ban went into force from midnight (2100 GMT Saturday) "in accordance with the principle of reciprocity", SANA state news agency said, although Turkey has said its airspace remains open to Syrian civilian flights.
Since last Wednesday, Turkey had warned its airlines to avoid Syrian airspace for fear of retaliation for that day's interception of the Syrian Air flight by Turkish jets on the allegation it was carrying military equipment.
The United States backed its NATO ally's confiscation of what Russia said was radar spare parts, saying they constituted "serious military equipment".
Russia, traditional ally of President Bashar al-Assad's regime, insisted the cargo broke no international rules.
Turkey has taken an increasingly strident line towards its southern neighbour since a shell fired from the Syrian side of the border killed five of its nationals on October 3.
It has since repeatedly retaliated for cross-border fire, prompting growing UN concern and a flurry of diplomatic contacts.
After talks with his German counterpart Guido Westerwelle on Saturday, Turkish Foreign Minister Ahmet Davutoglu reiterated that Ankara would not tolerate any further border incidents.
"We will hit back without hesitation if we believe Turkey's national security is in danger," he said.
Westerwelle renewed Germany's support for its NATO ally while at the same time appealing for restraint. "We are on Turkey's side but we also call on Turkey to show moderation," he said.
COMMENTS (6)
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@Feeka: Correction: Turkey is a secular country. (Not sure for how much longer though).
Turkish (a muslim country) killing muslim syrians - can Pakistan intervene to help resolve the issue.
@Moise
So you think Israel controls Turkey and all of the Arab Countries? The reality is that Saudi Arabia and Turkey are leading the charge against Syria - Israel doesn't have to lift a finger.
@Moise: no muhammed
@CallinArmy-Khi: Cos Israel said so?
syria -has got to go!!