Military engineers and civilian support staff took leave of Prince Sultan Air Base in al-Kharj, 80km south of Riyadh, in a low-key ceremony.
Lieutenant Gary Arasin, a spokesman at Shaw Air Force Base who attended the ceremony, said there were very few staff left, "probably just a couple of hundred".
The base was the home of the largest US air operations in the region with a state-of-the-art command centre and squadrons of fighter jets, AWACS radar surveillance and tanker planes.
The removal of US troops comes within a decade of al-Qaida leader Usama bin Ladin’s vow to drive American troops out of his native country.
The Pentagon invested millions in fortifying the base in 1996 after a truck bomb devastated a US military housing complex in Dhahran, killing 17 US service members.
But the size of US military presence in the Gulf remains the same, with huge bases in Oman, Bahrain, Kuwait, Iraq and Afghanistan in addition to a command and control centre in Qatar.
Around 50 trucks were queueing up outside the base ready to move remaining US military equipment to Qatar.
Twelve year history
The Prince Sultan Air Base used to house thousands of US and foreign troops operating in the kingdom since the 1991 Gulf War.
Washington agreed to withdraw several thousand of its troops stationed in Saudi Arabia in May, following a visit by US Defense Secretary Donald Rumsfeld.
Media were kept out of the base on Tuesday, in keeping with a long-standing Saudi policy of downplaying the Western military presence in the conservative kingdom.
Placards bearing the sign "welcome to coalition forces" have been dumped next to the road leading to the camp.
A dozen or so French training monitors involved in giving rescue training to Saudi military personnel and in helicopter maintenance remain at Prince Sultan Air Base, the Western sources said.