The pilot landed his plane at the King Hussein military airbase 80 km (50 miles) northeast of Amman and immediately asked for sanctuary, Jordanian officials told Reuters.
"He is being debriefed at the moment," Jordan's Minister of State for Information Samih al-Maaytah said.
The defection will boost the morale of the rebel movement fighting Assad at a time when government forces are intensifying efforts to crush the uprising and international peace efforts are stalled.
Thousands of soldiers have deserted government ranks in the 15 months since the revolt broke out and they now form the backbone of the rebel army. But unlike last year's uprisings in Libya and Yemen, no members of Assad's inner circle have broken with him.
Syria denounces 'traitor'
Syria on Thursday denounced an air force pilot who defected as a "traitor" and said it wanted to recover the warplane he used to flee into neighbouring Jordan.
"The pilot is considered a deserter and a traitor to his country, and to his military honour, and he will be sanctioned under military rules," state television quoted the defence ministry as saying.
Syrian towns continue to see bombings
Elsewhere on Thursday, the Syrian army maintained its bombardment of downtown areas of Homs even though a temporary truce had been agreed to allow aid workers to evacuate the sick and wounded.
The International Committee of the Red Cross said its aid workers had been forced to turn back on the way into Hom's old city because of shooting but would try again later in the day.
"The shelling across the city has been relentless since last night, intensifying this morning. The army has no intention of relieving the humanitarian situation. They want Homs destroyed," activist Abu Salah told Reuters from Homs.
The pro-opposition Syrian Observatory for Human Rights said 31 people were killed around the country during the day, with at least 10 of them in Homs.
Drop the pilot
Syrian state television named the pilot who defected as Colonel Hassan Hamada. Communications were lost with his plane while he was on a training mission near the border with Jordan, it said.
Opposition sources said Hamada is a 44-year-old Sunni Muslim from Idlib province and he had smuggled his family to Turkey before his dramatic defection.
His hometown Kfar Takharim has been repeatedly shelled in the past several months and suffered intense artillery and helicopter bombardments in the last few days, opposition campaigners who spoke to his family said.
Many air force personnel and well as army soldiers are from Syria's Sunni majority, although intelligence and senior officers are largely Alawite, the minority sect to which Assad and his family belong and which forms their powerbase.
The International Institute for Strategic Studies says the air force has 365 combat capable aircraft, including 50 MiG-23 Flogger and MiG-29 Fulcrum fighters and 40,000 personnel.
The most prominent defection so far in the conflict was that of Colonel Riad al-Asaad last July, who helped set up the rebel Free Syria Army after taking refuge in Turkey.
Last week Brigadier General Ahmad Berro, head of a tank unit in Aleppo province, fled with his family to Turkey.
Though a boost to Assad's foes, the pilot's defection could complicate the international scenarios of a conflict that many governments fear could spill over Syria's border and spread though the already volatile Middle East.
A Jordanian official, speaking on condition of anonymity, said the incident was "difficult to handle". Amman is nervous over a possible Syrian military reaction after months of border tension as thousands of Syrians flee the crackdown to Jordan.
Morning barrage
In Homs, dawn broke to heavy shelling but the barrages eased up during the day, resident Waleed Faris said.
"Now I can hear one or two mortars fall every half an hour. It is quiet today compared to the past few days," he said.
Two people were killed in his neighborhood of Khalidiya on Thursday, he said.
Homs has been at the center of the revolt against four decades of dynastic rule by the Assad family and became the focus of world concern in February and March when opposition-held neighbourhoods endured weeks of government bombardments and sniper fire in which hundreds of people were killed.
In other violence on Thursday, activists said 10 people were killed when government forces rained shells on the village Enkhel in the southern Deraa province, birthplace of the revolt.
Video posted on the Internet showed nine bodies wrapped in blankets and surrounded by weeping men and women.
Syrian state news agency SANA said 19 law enforcement members and civilians were buried on Thursday.
The United Nations says more than 10,000 people have been killed by Assad's forces during the conflict. The government says at least 2,600 members of the military and security forces have been killed by what it characterizes as a plot by foreign-backed "Islamist terrorists" to bring it down.
With a joint UN-Arab League ceasefire plan in tatters and the international community divided, world leaders and diplomats have been unable to stop the bloodshed.
The Arab League's deputy secretary general, Ahmed Ben Helli, criticized Russia on Thursday for selling arms to Syria and said that UN sanctions could be needed to force Assad and the rebels to implement international envoy Kofi Annan's peace plan.
"Any assistance in aiding violence should be stopped. When you deliver military equipment you are helping to kill people. That should be stopped," he told Russia's Interfax news agency.
Russia, one of Assad's main suppliers of military equipment, has shielded its long-standing ally Syria from tougher UN sanctions. It says the solution must come through political dialogue, an approach most of the Syrian opposition rejects.
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@Michael Rivero: Take a bath - smell will go away.
I smell a setup. I'll wager this "Defecting pilot" (Reg Trademark Mossad) will "confess" to Assad's "war crimes" (Reg Trademark CIA) to sell a gullible public yet another pointless war.