Johnson and three other U.S. soldiers were killed when their patrol of 12 U.S. and 30 Nigerien forces was ambushed by an ISIS-affiliated group when leaving the village of Tongo Tongo on Oct. 4.
"We can confirm that the Armed Forces Medical Examiner has positively identified these remains as those of Sgt. Johnson," Dana W. White, the chief Department of Defense spokesperson, said in a statement today. "The department continues to conduct a detailed and thorough investigation into the deaths of Staff Sgt. Bryan C. Black, Staff Sgt. Jeremiah W. Johnson, Staff Sgt. Dustin M. Wright and Sgt. La David T. Johnson. We extend our deepest condolences to all of the families of the fallen."
The U.S. official said Johnson's family has been notified of the discovery.
Last month Johnson's widow, Myeshia Johnson, told ABC News she was prevented from viewing his remains before he was buried in his home state of Florida on Oct. 21.
She added, "They won't show me a finger, a hand. I know my husband's body from head to toe, and they won't let me see anything. I don't know what's in that box. It could be empty for all I know, but I need to see my husband. I haven't seen him since he came home."
A team of U.S. Africa Command and Nigerien military investigators visited the site of the ambush on Nov. 12 as part of the investigation, which the U.S. Army expects to conclude in January.
"As part of its mission, the AFRICOM investigation team interviewed local villagers, conducted a physical examination of multiple areas of interest related to the attack and retraced actions leading up to, during and after this ambush," U.S. Africa Command said in a press release.
According to the U.S. official, Johnson's body was not located until two days after the attack. In circumstances that remain unclear, he became separated from the rest of the patrol. The village later turned over his body to the Nigerien military.