The court in the resort town of Bodrum found Syrian nationals Muwafaka Alabash, 36, and Asem Alfrhad, 35, guilty of trafficking migrants and sentenced them to four years and two months, the Dogan News Agency said.
But it cleared them of causing the death of five people "through deliberate negligence", a charge that carried a sentence of up to 35 years in prison.
He drowned after his family decided in early September to make the risky journey across the Aegean Sea from Turkey to Greece in an overloaded open boat.
Aylan's mother Rihana and brother Ghaleb, four, and two others also died in the same accident as they attempted the crossing from Bodrum to the island of Kos.
Aylan's father Abdullah Kurdi had been implicated in the tragedy, with Turkish authorities originally accusing him in absentia of being responsible for the deaths and driving the boat at the time of the disaster.
A lawyer for the defendants, Kemal Ertugrul, said the pair would not have been jailed if they were Turkish and reaffirmed the past accusations against Abdullah Kurdi.
"There is one name missing from the real organisers and culprits," he said.
"Nobody is looking for him. All the witnesses and those who experienced the disaster said the organiser is Abdullah Kurdi. Therefore I will file a criminal complaint against him."
Asem Alfrhad said during the trial Abdullah Kurdi was the "the real criminal here... Who became a hero on television but did not even testify."
Kurdi became a prominent figure through media interviews following Aylan's death and delivered an "alternative" Christmas message in Britain in 2015, aired on a rival channel at the same time as Queen Elizabeth II's traditional address.
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