Interior Ministry spokesman Lufullah Mashal, told Reuters on Sunday the bodies of the men, one of them Swiss, were discovered in Baghe Chilstone, an ancient garden not far from the city's centre.
"Locals informed the police and showed them the bodies and an investigation is going on as to who stoned these to death, and why," Mashal said.
"One of them holds a Swiss passport and the nationality of the other is not known."
Both had come from neighbouring Pakistan nine days ago, said Khalil Aminzada, deputy chief of Kabul police.
He said the two were wearing local shalwar (baggy trousers) and long shirts as well as woollen hats.
The two were pelted on Saturday night with bricks and stones and their bodies were being examined by local forensic experts, he added.