Prosecutors in Traunstein, near the Austrian border, accused the men of "professional smuggling of people resulting in death."
The court on Friday sentenced the 27-year-old main defendant to four years' imprisonment, while the boatman was handed a two-and-a-half-year jail term. A third man, who had a previous conviction for trafficking, and who acted as a liaison for families, was put on two years' probation.
The three organized smuggling trips between Izmir in Turkey and the Greece coastline across the Mediterranean. During one fateful trip in September, 2015, an unlit dinghy overloaded with refugees struck a freighter near the Greek island of Lesbos and 13 people died, Two children remain missing.
The main suspect in the case, a Syrian national in Turkey, was charged with organizing the dangerous boat trips. The boatman was himself a refugee and was offered free travel in return for piloting the dinghy while the third liaised with the family members of the refugees in Germany.
The three defendants had come to Germany as refugees themselves.