The accident happened last month in a village near Uijongbu, 30 kilometres (18 miles) south of South Korea's heavily fortified border with North Korea.
It has prompted several anti-US demonstrations by South Korean protesters and an apology from the US military.
The US has 37,000 troops in South Korea to deter any invasion by the North.
The protesters, some of whom attacked and injured South Korean police guarding the US army base at Uijongbu, said the drivers of the vehicle had deliberately killed the girls and demanded the soldiers be handed over to local police.
Village road
The United States Forces Korea (USFK) said in a statement that Sergeant Mark Walker and Sergeant Fernando Nino of the 8th US Army 2nd Infantry division were charged with "negligent homicide" in the deaths of teenagers Shim Mi-son and Shin Hyo-sun.
"Both are charged with the deaths of the two girls by negligently failing to ensure the safe operation of the vehicle," the statement said.
Sergeant Walker was the driver and Sergeant Nino the track commander of the tank-like minesweeping vehicle which ran over the girls on a village road
It was not clear where in the US the two men come from.
On Wednesday, USFK commander General Leon LaPorte, issued the latest of several formal US apologies for the incident.
"The US army accepts full responsibility for this tragic accident," his statement said.
"I apologise for the grief and sorrow we've inflicted on these two families, which is indescribable."
South Korea has no jurisdiction over US military personnel involved in accidents while on duty. Occasional accidents and crimes have prompted demands from civic groups to give South Korea more legal power in cases involving US troops.