The couple were on their way with four others to the veterinarian's office to immunise some of their cattle when they were kidnapped. The convoy was besieged by a group of armed men, who let their companions go free but took the Germans.
The victims were killed shortly after the kidnapping happened on Wednesday.
According to local media reports, those responsible belong to the Paraguayan People's Army (EPP), a communist guerrilla movement, though no arrests have been made.
Paraguay's interior minister Francisco José De Vargas Benítez reported on Thursday that both victims were found with gun wounds in the back. An investigation said they were shot at close range, though an autopsy is still to be performed.
The German couple, aged 60 and 52, had lived in the South American country on their small cattle ranch for more than a decde, reported Bild.