The soldier, identified as Major Hassan Malik, opened fire with two handguns in a busy processing center where troops go before being deployed on overseas missions in Iraq and Afghanistan.
Speaking to reporters, Lt Gen Bob Cone at Fort Hood, said that the motive for the attack remained unclear.
"We don't know that right now. Again, this is all under investigation," he stressed, adding he believed the incident was now over.
General Cone confirmed that 12 people were dead. Two other soldiers were arrested after the shooting spree and were being held as suspects, he added.
The violence was believed to be the worst mass shooting in history at a US military base.