Cypriot club Larnaca were fined 50,000 euros ($58,680) and also face a partial closure of their stadium for their next UEFA club competition home fixture, for their fans' chants during the round-of-16 tie with Palace in March.
Ukraine's Shakhtar were handed a 30,000-euro fine and their partial stadium closure was suspended for a probationary period of two years for what UEFA described as an "illicit banner" displayed during the semi-final first leg in April, when their home leg was played in Krakow, Poland.
Shakhtar were also fined 4,000 euros for the lighting of fireworks.
Crystal Palace will play Rayo Vallecano in the Conference League final on May 27 in Leipzig.