Lt. Col. Paul Voss, 46, of Yigo, Guam, served at Headquarters Air Combat Command at Joint Base Langley-Eustis, Virginia, and Capt. Ryan Phaneuf, 30, of Hudson, New Hampshire, served on the 37th Bomb Squadron at Ellsworth Air Force Base, South Dakota, the Pentagon said in a statement.
The Pentagon added that the men had been supporting Operation Freedom's Sentinel, the military's official designation for the US mission in Afghanistan.
The men died in the crash of a Bombardier E-11A aircraft in Afghanistan's Ghazni province, according to the statement. The E-11A is used to link troops in the field to headquarters and has been previously described by Air Force pilots as "WiFi in the sky."
The US military said Tuesday that two bodies had been recovered from the crash by US forces, adding that sensitive equipment also had been disabled by military personnel who arrived at the site.
A defense official had previously told CNN there was an indication that the crew had made a distress call, a sign of some type of trouble with the aircraft, prior to its crashing.
A spokesperson for US forces in Afghanistan said Monday that there was "no indication" the plane had been downed by enemy fire.
"A U.S. Bombardier E-11A crashed today in Ghazni province, Afghanistan. While the cause of crash is under investigation, there are no indications the crash was caused by enemy fire. We will provide additional information as it becomes available," Col. Sonny Leggett said in a tweet.
"Taliban claims that additional aircraft have crashed are false," he added.