Mykola Protasov was sentenced to 13 years in jail while Valeriy Kostenko and Oleksandr Popovych each received 12-year sentences.
Gongadze's beheaded body was found in a forest outside Kiev in November 2000.
Gongadze crusaded against official corruption. His killing triggered months of protests after Mykola Melnychenko, a former bodyguard to then-President Leonid Kuchma, released tape recordings in which voices resembling those of Kuchma and others were heard conspiring against the journalist.
Oleksiy Pukach, the former chief of the Interior Ministry's surveillance department, is also wanted for the murder and is being sought on an international warrant.
Investigations have failed to track down those who ordered the killing.