The German defence ministry and a parliamentary committee are also investigating Kurnaz's allegations. The two suspects will now be questioned, prosecutor Walter Vollmer said.
They said they were investigating one soldier whom Kurnaz had identified through photographs and another who was on duty with him.
"Both suspects are accused of grievous bodily harm while on duty," the prosecutors said in a statement.
Kurnaz, born in Germany in 1982, was in the process of acquiring German citizenship when he was arrested in Pakistan in late 2001.
He says he also suffered abuse at Guantanamo Bay, where the United States has held suspects indefinitely without charge.
The Kurnaz case puts Germany in a compromising position as the country also faces allegations that its previous government secretly aided a US programme to kidnap and fly terrorism suspects to third countries for interrogation.