Lt Gen Abulaziz al-Shalal is one of the highest-ranking officials to join the uprising against the Syrian regime.
The army had failed to protect Syrians and turned into “gangs of murder”, the general said in a video statement.
The announcement comes as rebels claim to have made further gains in parts of the country.
Meanwhile, the UN peace envoy for Syria has met opposition figures in Damascus in a new bid to end the conflict.
After reportedly crossing the border into Turkey, the commander released a statement saying he had defected because the military had perpetrated massacres in towns and villages instead of protecting Syrians.
“I declare my defection from the army because of its deviation from its fundamental mission to protect the nation and transformation into gangs of murder and destruction,” he said in a video message posted online.
Opposition sources said the commander had been secretly co-operating with the rebels from the outset, the BBC’s Middle East correspondent Jim Muir reports.
This is believed to be the case with many other senior defectors, our correspondent adds.
But Gen Shalal said defecting was becoming increasingly difficult because of the increased level of surveillance
“Definitely, there are other high-ranking officers who want to defect but the situation is not suitable for them to declare defection,” he said.
An unnamed Syrian security source confirmed the army chief’s defection but played down its significance, Reuters news agency reports.
Gen Shalal was due to retire soon and joined the uprising to “play hero”, the source is quoted as saying.
The development comes amid reports of rebel fighters seizing the north-western town of Harem near the Turkish border.
President, Bashar al-Assad met UN peace envoy for Syria Lakhdar Brahimi in Damascus
Earlier this week, opposition activists said dozens of people had been killed in a government air strike in the rebel-held town of Halfaya in Hama province.
Although rebels have claimed some major territorial gains in recent months, the regime has hit back with massive firepower at the areas it has lost.
Meanwhile, the UN peace envoy for Syria Lakhdar Brahimi held talks in Damascus with opposition figures who are tolerated by the regime but not supported by the mainstream opposition, our correspondent says.
Earlier, Mr Brahimi had also met President Assad to discuss “the many steps to be taken in the future” to help end the conflict.
He did not, however, elaborate on what these steps were.
With the government dismissing the uprising as a foreign-backed extremist plot, and the rebels demanding that President Assad leave power immediately, the chances for a peaceful compromise seem slight, our correspondent says.
Rebels have been fighting Mr Assad’s government for 21 months.