The troops -- a small number remaining from 1,430 initially deployed last August in Iraq -- crossed the border into Kuwait shortly before 1300 GMT, Defence Minister Jose Bono announced in Madrid.
"I received a call from General Munoz (leading the Spanish contingent) at 2:57 pm telling me he had carried out his orders," he said. "There are no more Spanish soldiers in Iraq."
Defence ministry sources said the troops were expected to arrive back in Spain on Monday afternoon.
The withdrawal is the fulfillment of an election pledge by Prime Minister Jose Luis Rodriguez Zapatero to Spaniards who massively opposed the country's participation in the US-led invasion and occupation of Iraq.
Zapatero's socialists scored an upset election victory in March.
A large convoy of Spanish armoured vehicles and troops entered the Navistar military crossing point, near the Kuwaiti border post of Abdali, at midday after leaving their base at Diwaniyah in southern Iraq.
Some 10 buses carrying soldiers, about a dozen military vehicles with mounted machine-guns, two dozen armoured personnel carriers and numerous military jeeps were seen heading toward Kuwait.
A US-led coalition spokesman told AFP in Kuwait that the convoy had begun its journey at sunrise from Diwaniyah.
Zapatero said last week he was glad he had decided to withdraw his country's troops from Iraq, especially given the upsurge in violence and a scandal over the abuse of Iraqi prisoners by coalition soldiers.
Zapatero told parliament the pullout "is a decision with which I am increasingly satisfied for having made it when I did".
He rode to victory in the elections on a wave of anger after 191 people were killed and nearly 2,000 injured in train bombings in Madrid on March 11, widely perceived here as having been carried out to punish Spain for its support of the US-led coalition.
On taking office, Zapatero vowed to withdraw the Spanish contingent from Iraq, unless the United Nations took political and military control of the country before June 30, but he then decided to press ahead with the withdrawal as soon as possible.
The bulk of the Spanish contingent left the country on April 28, with a small number of troops staying behind to complete the operation.
Spanish soldiers finished withdrawing from their base in the southern Shiite Muslim holy city of Najaf on April 27 and Spanish forces transferred operations at Diwaniyah to US forces last Sunday.
Zapatero's insistence on withdrawal overturned the policy of conservative predecessor Jose Maria Aznar, who had brushed aside anger from the electorate to back Washington.
But the decision to pull out dented the US-led coalition, with Honduras and the Dominican Republic following Madrid's lead and also moving to recall their troops.
Washington has so far not found any country willing to contribute new troops to replace those who have left.
Meanwhile, a correspondent with Spanish national radio RNE who was reporting on the troop pullout was released after being briefly detained at a mosque in Najaf by a group close to rebel cleric Moqtada Sadr.
"He is free and he is fine," the radio said of Fran Sevilla, who was released after around four hours in captivity.
"Fortunately, Sevilla was not in a dangerous situation," said the station's news director Javier Arenas.
The Spanish government issued a statement saying it welcomed the release.
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