Nawaf al-Fares is the first senior Syrian diplomat to abandon the government of President Bashar al-Assad.
Syria’s foreign affairs ministry has responded by dismissing him from his post, Sana news agency says.
Meanwhile Western nations are urging the UN to threaten tough sanctions against Syria.
They want a 10-day sanctions ultimatum to be part of a Security Council resolution on the future of the UN’s observer mission in the country. A new resolution must be passed before the mission’s mandate ends on Friday next week.
Nawaf al-Fares’s defection comes just a week after a Syrian general from a powerful family close to President Bashar al-Assad also defected.
He confirmed his decision in a statement broadcast on Facebook and al-Jazeera TV.
With Syrian revolutionary flags behind him, he read out the statement saying he was resigning both as Syria’s ambassador to Iraq and as a member of the ruling Baath Party.
“I call on all party members to do the same because the regime has transformed it into a tool to oppress the people and their aspirations to freedom and dignity.
“I announce, from this moment on, that I am siding with the people’s revolution in Syria, my natural place in these difficult circumstances which Syria is going through.”
Syria’s foreign ministry said he had made statements that contradicted the duties of his post and no longer had any relation to the Syrian embassy in Baghdad.
Nawaf al-Fares was appointed ambassador to Baghdad in 2008.
He is also chief of a Sunni tribe, the Uqaydat, which straddles Syria’s eastern border with Iraq.
That area, around the city of Deir al-Zour, has become a hotbed of support for the rebels and has been heavily bombarded in recent weeks.
Syria has been convulsed by internal conflict since protests against President basher al-Assad began early last year. The protests turned into an armed rebellion and thousands of people have been killed.
Last week, senior army officer Brig. Gen. Manaf Tlas fled Syria via Turkey.
He was a commander of a unit of the elite Republican Guard and as a young man he attended military training with President Bashar al-Assad.
Gen. Manaf Tlas had been under a form of home arrest since May 2011 because he opposed security measures imposed by the regime, sources said.
Meanwhile, Western nations are pressing the UN to threaten Damascus with sanctions as it considers renewing the mandate for its observer mission in Syria which expires on 20 July.
The mission had a 90-day remit to monitor a truce, but fighting has continued largely unabated.
The truce formed part of a six-point peace plan brokered by UN-Arab League envoy Kofi Annan, who has called for “clear consequences” for the Syrian government and rebels if the ceasefire is not observed.
Russia has suggested a 90-day extension. But Western states say a simple rollover of the mission is not enough.
A draft resolution has been circulated threatening Damascus with sanctions within 10 days, if it fails to stop using heavy weapons and pull back its troops from towns and cities.
The UK’s envoy to the UN, Mark Lyall Grant, told reporters that Britain, France, the US and Germany would propose making compliance with the ceasefire mandatory under Chapter 7 of the UN charter.
Last week, more than 100 countries called on the Security Council to invoke Article 41 of the Charter, which stops short of military intervention.
Russia has said use of Chapter 7 is a “last resort”. China, which like Russia has vetoed the two previous attempts to impose tougher measures, has said it would support a rollover of the mission.
The New York Times: Syria’s Ambassador to Iraq Reported to Defect
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