Pejcic hit 1.3 rounds more than Denmark's Stina Nielsen, who came in second.
An Olympian bronze-medal winner in Beijing in 2008, Pejcic entered the finals as the last contender but managed to come in first place.
Russia's Darija-Vdovina took the bronze in Maribor on Friday.
Pejcic's victory was even greater after taking the silver in the air rifle team event along with Valentina Gustin and Marta Zeljkovic, who made up Croatia's team.