The court sentenced them to four years and two months jail, although their lawyer said they were not expected to serve time in prison as they had already been detained for several months.
Two other pilots and a flight attendant were acquitted, while charges were dropped against another flight attendant.
Ghosn, once a leading light of the global car industry, was arrested in Japan in late 2018 and charged with underreporting his salary and using company funds for personal purposes, charges he denies.
The ousted chairman of the alliance of Renault, Nissan Motor Co and Mitsubishi Motors Corp had been awaiting trial under house arrest in Japan when he escaped in December 2019 via Istanbul to Beirut, his childhood home.
Ghosn, who holds French, Lebanese and Brazilian citizenship, is still a fugitive and remains in Beirut, where he announced several months ago that he was launching a university business programme. Lebanon does not have an extradition treaty with Japan.
An executive from Turkish private jet operator MNG Jet and four pilots were detained by Turkish authorities in early January 2020 and charged with migrant smuggling. Slideshow ( 2 images )
The lawyer for one of the convicted pilots, Erem Yucel, told reporters they would appeal the verdict.
Convicted pilot Noyan Pasin said that staff and officials had not suspected anything was wrong with the flight, either in Japan or Turkey, so it was wrong to single out the pilots.
“We were expected to be suspicious and were sentenced because we weren’t suspicious,” he told reporters.
The defendants were released in July, when the first hearing was held, and are not expected to return to jail due to time they served. Japan is not known to have requested their extradition to face charges there.
The Ghosn saga has shaken the global auto industry, at one point jeopardising the Renault-Nissan alliance which he masterminded, and increased scrutiny of Japan’s judicial system.
Renault and Nissan have struggled to recover profitability following his tenure, during which both automakers say Ghosn focused too much on expanding sales and market share. Reporting by Ezgi Erkoyun; Writing by Ali Kucukgocmen; Editing by Daren Butler, Jonathan Spicer and Angus MacSwan