The Norwegian was perfect in shooting, finishing 11.4 seconds ahead of Martin Fourcade of France, who kept his overall lead in the World Cup. Third place went to another Frenchman, Fabien Claude (+25.6).
Slovenia's best biathlete Jakov Fak finished 2 minutes and 20.2 seconds behind the winner for the 12th place, as he missed one target in the process. The second best Slovenia was Rok Tršan (+4:26.1) in 31st place.
Boe, who was absent from the World Cup for four weeks after becoming a father, said he "started slower than usual today" and "spent some more time on the shooting range, but everything went well and I'm happy."
He added that Fourcade had rang up four wins in the meantime, which made it difficult for him to grab the overall win. "This is why the world championship is the primary goal."
Fak, who kept his 15th overall place in the World Cup, said that "missing the last shot was very painful" as he had some technical problems. "It will be hard to climb higher this season, and today I tried to make a better result, but I couldn't."
The races at the plateau within the Triglav National Park continue on Friday with the women's 15km individual event.
Saturday is reserved for the single mixed relay and the 4×7.5km mixed relay, with the meet wrapping up on Sunday with the men's 15km mass start and a women's 12.5km mass start competitions.