Khalidi, whose full title is given as "Pilot Major General," was shot as he got out of his car in the capital's Rukn-Eddin neighborhood, SANA news agency reported.
State television said that the "assassination" happened late on Monday, according to Agence France-Presse.
The TV report said Khalidi was killed as part of a rebel "campaign to target national personalities and scientists."
Al-Khalidi was described as "one of Syria's foremost experts in aviation."
Yet activists told Al Jazeera that Khalidi was planning to defect, "so the regime got rid of him before he does that."
As GlobalPost has reported, the Syrian air force has played a prominent role in the government's fight against its opponents.
Just Monday, warplanes were reported to have repeatedly bombed rebel forces outside Damascus. GlobalPost correspondent Tracey Shelton says the "near constant barrage of regime attacks from the air" terrorizes civilians.
Reuters reported Tuesday that airstrikes on Damascus and other cities had resumed with "renewed intensity" since the official end of the failed Eid ceasefire.
The attack on Khalidi, if confirmed, would not be the first instance of rebels targeting senior regime officials.
In July, Syria's defense minister, Daoud Rajha, and Assef Shawkat, his deputy and President Bashar al-Assad's brother-in-law, were killed in a suicide bombing in Damascus.
Both the Free Syrian Army and the Islamist rebel group Liwa al-Islam claimed responsibility for that attack.