Škubonja attended the Higher Film School in Belgrade and graduated as a director from the Belgrade Academy of Drama Arts. He did not make many films and the peak of his career was the film for children Izgubljena olovka (1960), which won awards on festivals in Venice, Mar del Plata and Cannes. His comedy for children Veliko suđenje (1961) was judged unfavorably, while his drama Nizvodno od sunca (1969) won the Great Golden Arena in Pula. For all his films the screenplays were written by his wife Stanislava Borisavljević.