The air force is considered fiercely loyal to Assad's regime, and the defection suggests some of Syria's most ironclad allegiances are fraying.
It was a triumph for the rebels fighting to overthrow Assad. A spokesman for the rebel Free Syrian Army, Ahmad Kassem, said the group had encouraged the pilot to defect and monitored his activity until the jet landed safely in Jordan.
The pilot, identified as Colonel Hassan Hammadeh, removed his air force tag and kneeled on the tarmac in prayer after landing his plane at King Hussein Air Base in Mafraq, Jordan, 70km north of Amman, a Jordanian security official said.
He said Jordanian official were questioning the defector, but he will be allowed to stay in the country on "humanitarian grounds."
"He was given asylum because if he returned home, his safety will not be guaranteed. He may tortured or killed," the official said. He declined to say what Jordan will do with the jet. The official insisted on anonymity, citing the sensitivity of the matter.