The 56-year-old Syrian colonel managed to jump out of the aircraft after pulling his parachute as the plane was going down above the Hatay province in southern Turkey.
The colonel -- who was flying alone when the plane crashed -- is charged with "spying" and "violation of the Turkish Republic's border security", state-run news agency Anadolu said.
The Syrian rebel group Ahrar al-Sham said at the time it shot down the regime plane which had been flying over Idlib province in northwestern Syria and carrying out air strikes.
The pilot was discharged from hospital after treatment and ordered by a local court to be remanded in custody ahead of trial.
The arrest comes after US President Donald Trump launched a strike in Syria in retaliation for a "barbaric" chemical attack he blamed on Syrian President Bashar al-Assad.
The Turkish health ministry said on Thursday that initial findings pointed to the use of sarin nerve agent in the attack on the rebel-held town of Khan Sheikhun in Idlib which killed dozens and left hundreds more injured.
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