The final convoy consisted of 110 vehicles carrying over 500 soldiers according to media reports.
The convoy's arrival in Kuwait marked the end of a week of events commemorating the end of the US mission in Iraq.
In his weekly address on Saturday, Obama thanked troops who had served in Iraq during the almost nine-year long mission.
"More than 1.5 million Americans have served there with honor, skill, and bravery; tens of thousands have been wounded. Military families have sacrificed greatly – none more so than the families of those nearly 4,500 Americans who made the ultimate sacrifice," Obama had said.
"All of them – our troops, veterans, and their families – will always have the thanks of a grateful nation," he added.
On Thursday, Secretary of Defense Leon Panetta marked the war's end in a ceremony held at Baghdad international airport.
Panetta praised American troops and said their work had "not been in vain."
"You will leave with great pride — lasting pride, secure in knowing that your sacrifice has helped the Iraqi people to cast tyranny aside and to offer hope for prosperity and peace to this country's future generations,” he said.
The president's campaign has touted the decision to pull troops from Iraq as "a promise kept" by Obama who opposed the war at its inception and as a candidate in 2008.
A video released Thursday highlighted a series of statements from Obama's 2008 campaign declaring his intent to end the war.
Many Republicans however have attacked the president for pulling troops and have called for a U.S. presence to remain in Iraq in part to counter Iranian influence in the region.
Sen. John McCainJohn McCainFive fights for Trump’s first year Trump wall faces skepticism on border No Congress members along Mexico border support funding Trump's wall MORE said the administration deserved "scorn" for withdrawing U.S. forces.
"It is clear that this decision of a complete pullout of United States troops from Iraq was dictated by politics, and not our national security interests," McCain said from the Senate floor on Wednesday. "I believe history will judge this president’s leadership with the scorn and disdain it deserves.”
More than 4,500 U.S. servicemen were killed and 32,000 wounded in the nine-year conflict.