Two children are still missing after the inflatable dinghy hit a freighter off the Greek island of Lesbos.
The 27-year-old who organised the crossing was jailed for four years.
The man steering the boat was given a two-and-a-half year sentenced. He had been offered free passage in return for taking the helm.
A third man received a suspended sentence. The boat was heading from Turkey to Greece.
The case came to a German court because one of the alleged smugglers was arrested in a refugee camp in Burghausen, in the country's south-east.
According to the prosecutor's office, at least 46 people were on board and five children were among the dead.
The prosecution had pushed for a longer sentence of 12 years and six months for the main defendant, according to German media.
However, presiding judge Erich Fuchs called him "a small fish" and said the man was a migrant himself who was not trying to make money, according to the Bayerischer Rundfunk broadcasting company.
Mr Fuchs said he had taken $100 per person (Â£77; 85 euros) and the rest of the much-larger fee was passed to a Turkish smuggling organisation.
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.
A German court has jailed two Syrian people traffickers over the deaths of 13 migrants in the Mediterranean in 2015.