The president's plane touched down at Andrews Air Force base just outside Washington at about 12.25am on Friday morning, before jetting on to his ranch in Crawford, Texas, according to an Air Force sergeant.
From start to finish, Bush's trip took a little over 30 hours, most of them spent in the air. With him were a handful of aides, US Secret Service agents and reporters, all of whom had been sworn to secrecy.
News of the visit was not even released until Air Force One had already left for fear of the sort of missile fire that forced an emergency landing by a DHL civilian cargo jet last week.
Troops of the 1st Armoured Division which patrols the area around the Iraqi capital leapt to their feet, threw their arms in the air and cheered when the surprise guest arrived at their US holiday feast.
"I was looking for a warm meal somewhere, thanks for inviting me to dinner," said the US commander in chief in his familiar "downhome" manner, to deafening applause from the troops.
"I can't think of a finer group of folks to be having Thanksgiving dinner with," Bush, with brightly coloured military standards behind him, told the soldiers from the 1st Armoured and 82nd Airborne divisions and the 2nd Armored Cavalry Regiment in a huge hangar-like mess hall at Baghdad airport.
"I bring a message on behalf of America, we thank you for your service," he told the troops, who have come under regular attack during the persistent guerrilla action that has dogged the US-led occupation for the past seven months.
"We didn't charge hundreds of miles into the heart of Iraq, and pay a bitter cost of casualties, defeat a ruthless dictator and liberate 25 million people only to retreat before a band of thugs and assassins," Bush cautioned.
"You're defeating the terrorists here in Iraq, so we don't have to face them in our own country," he added in reference to the administration's belief that Iraq is now on the front line of the global "war on terror", launched after the September 11, 2001 attacks in New York and Washington.
After a couple of hours, the president headed back to Texas
Soldiers who are facing far longer tours of duty than they were initially promised said they had been given a boost.
"After 13 months in theater, my morale had kind of sputtered," said Captain Mark St Laurent, 36. "Now I'm good for another two months."