South Sudan army admitted killing the US journalist while in combat with rebels in Kaya town near the border with Uganda.
The 26-year-old Christopher Allen was killed in the fight in Central Equatoria on Saturday.
The army spokesman, Brigadier General Lul Ruai, said the clashes claimed five lives from both sides, including the American citizen.
"On the side of the rebels, we counted two dead bodies plus the white man, while two died on government side plus four wounded," the Juba-based army official is quoted saying by the local daily the Juba Monitor.
Brig Ruai said the foreign journalist, who was later confirmed by the US State Department as an American citizen, was embedded with the rebels to cover the clashes.
He added that the body of the American was airlifted to Juba Military Hospital to establish further details about the American and how he got to South Sudan.
"The impression we are getting is that he was embedded with the rebels that came to attack Kaya. How he got to Kaya, how he contacted the rebels, is something that we have no ideas about," Brig Ruai said.
"We can confirm that US citizen Christopher Allen died in South Sudan on August 26, 2017 while working as a journalist."
International advocacy group Human Rights Watch criticised the killing of the American, saying it was a violation of the international humanitarian law.
The agency urged the leaders of the war-torn country to condemn the killing and hold the perpetrators to account.
South Sudan's media environment has remained precarious since the attainment of independence in 2011.
Mr Allen's killing has brought the number of journalists who have died of gunshot wounds in South Sudan to 11 since 2012.