Hribar produced a superb finish to win in 20.70 seconds, equalling Duje Draganja's Croatian record and finishing 0.11 seconds ahead of France's Maxime Grousset and Ukraine's Nikita Sheremet, who shared second place. Sheremet also set a new world junior record.
The victory completed Hribar's medal set in Lublin, after bronze in the 4x50m freestyle relay and silver in the 100m freestyle.
Hribar secured Croatia's 13th gold medal at European short course championships, and the first in 15 years since Sanja Jovanović's triumph in the 50m backstroke.
In Sunday's women's 50m freestyle final, 18-year-old Jana Pavalić placed eighth in 23.87 seconds. She swam one hundredth of a second slower than her personal best set in Saturday's semi-final.
Gold went to Poland's Katarzyna Wasick in 23.20, ahead of France's Beryl Gastaldello and Italy's Sara Curtis, who tied for silver in 23.41.