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 Col. 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, 45 miles (70 kilometers) 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.
Syria's state-run TV reported earlier in the day that authorities had lost contact with a MiG-21 that was on a training mission in the country. After it became clear the pilot had defected, the state-run news agency quoted an unnamed military official as saying he was "a traitor to his country and his military honor."
Jordanian Information Minister Sameeh Maaytah confirmed that the pilot had defected.
The defection is a sensitive issue for Jordan, which wants to avoid getting dragged into the Syrian conflict. Jordan already has taken in 125,000 Syrian refugees, including hundreds of army and police defectors, and Syria is seeking their return.
Syria is one of Jordan's largest Arab trade partners, with bilateral trade estimated at $470 million last year.
The Syrian regime has been hit with defections before, although none as dramatic as the fighter pilot's. Most have been low-level conscripts in the army.
In March, however, Turkish officials said that two Syrian generals, a colonel and two sergeants had defected from the army and crossed into Turkey. Also in March, Syria's deputy oil minister became the highest-ranking civilian official to join the opposition and urged his countrymen to "abandon this sinking ship" as the nation spiraled toward civil war.
Brig. Gen. Mostafa Ahmad al-Sheik, who fled to Turkey in January, was the highest ranking officer to bolt. In late August, Adnan Bakkour, the attorney general of the central city of Hama, appeared in a video announcing he had defected.
In January, Imad Ghalioun, a member of Syria's parliament, left the country to join the opposition saying the Syrian people are suffering sweeping human rights violations.