Jan P. Matuszyński's acclaimed film won the festival's main prize, while Jan Holoubek received the best first-feature award for his 25 Years of Innocence.
It means Poland has secured two out of 3KinoFest's three accolades.
The jury's special award went to Hungary's Külön falka (A Separate Pack), directed by Hajni Kis.
The judges, led by Tomasz Kolankiewicz, who is also the artistic director of Poland's main film festival, chose among 22 entries from the Czech Republic, Poland, Slovakia and Hungary.
The movies were evenly matched in terms of artistic merit, the chair of judges said.
Jan P. Matuszyński could not take part in the online awards gala, having left for Los Angeles to promote Leave No Traces ahead of next year's Oscars, producers said, according to PAP.
Meanwhile, Jan Holoubek thanked his filming crew and producers, noting the debut feature was a key movie for every director. He added he was pleased to have won an award in the Czech Republic, the country of his ancestors, PAP reported.
Leave No Traces is based on real-life events surrounding Grzegorz Przemyk, a Warsaw high school student who was beaten to death by communist police in May 1983, during martial law imposed by the authorities to crush the Solidarity freedom movement.
25 Years of Innocence tells the true story of a man who spent 18 years in jail after being falsely convicted of murder.
Founded in 2014, the 3KinoFest's co-organisers include the Visegrad Fund, Polish Institute in Prague, The Czech-Polish Forum, Polish Film Institute (PISF) and Poland's Ministry of Culture and National Heritage, PAP reported.
(pm)
Source: PAP, 3kino.cz