The dead gunman had been named as Major Malik Nadal Hasan, a 39-year-old army psychiatrist.
Al Jazeera's Josh Rushing, reporting from Fort Hood, said there was no indication of motive for the unprecedented attack, which he said had left an atmosphere of "shock and fear" at the base.
April 3, 2009: Jiverly Wong, a Vietnamese immigrant, opens fire at an immigrant community centre in Binghamton, New York, killing 11 immigrants and two workers. Wong killed himself at the scene
March 10, 2009: Michael McLendon, 28, killed 10 people, including his
Mother and four other family members in Alabama before himself committing suicide.
February 14, 2008: Former student Steven Kazmierczak, 27, kills five students and wound 18 more in shooting at Northern Illinois University in DeKalb. He then killed himself.
December 5, 2007: Robert A. Hawkins, 19, opens fire in a shopping mall in Omaha, Nebraska killing eight people before taking his own life.
April 16, 2007: Cho Seung-Hui, 23, kills 32 students and staff at Virginia Tech before killing himself in the deadliest mass shooting in modern US history.
According to military officials, Hasan had been about to deploy overseas, although it was unclear if he was destined for Iraq or Afghanistan or when he was scheduled to leave.
Fort Hood was locked down after the attack, which occurred on the same day as a graduation ceremony was due to go ahead at the facility.
Some other bases across the US also stepped up security in the wake of the shootings.
Christopher Hogue, chief of media at Fort Hood, told reporters: "The only one we know who was shooting was killed and he had two handguns."
The alleged shooter was included in the total of 12 killed.
Barack Obama, the US president, called the attack a "horrific outburst of violence".
"It is horrifying that they should come under fire at an army base on American soil," he said in Washington.
Patty Culhane, Al Jazeera's correspondent in Washington, said that the attack had come in spite of rigorous security protocols at the base.
"At every US military base since September 11, they do something that is called '100 per cent ID check' - that means that when you pull up to the gate, there are armed soldiers and also contractors there, and you have to have a special sticker in your car," she said.
"You also have to have a military ID. If you do not have that, you have to pull over to the side, and your care is usually swept for explosives, and you need an escort.
"Family members [of service personnel] do have ID, so they are allowed to go on to the base."
Fort Hood is home to about 50,000 troops, although Kay Bailey Hutchison, a Texas senator, said there were about 35,000 troops at the base at the time.
"Our dedicated military personnel have sacrificed so much in service to our country, and it sickens me that the men and women of Fort Hood have been subjected to this senseless, random violence," she said.