The Norwegian was perfect on the range and came home in 24:56.8 minutes, 22.8 seconds ahead of France's Quentin Fillon Maillet in second place.
"It was the perfect day," said the 26-year-old winner. "I lead from the start and finally I shot ten in the sprint.
"I have to take small steps because my competitors rarely fail. For me, it's about winning each race which is the only way I can win overall."
Tarjei Boe secured the final podium spot, finishing just over a minute behind his younger brother.
Frenchman Martin Fourcade remains in control of the yellow bib on 826 points after 18 races, despite his sixth-placed finish on the day, with Maillet trailing his countryman on 766 points and JT Boe on 750 points.
Watch - Nové Mesto na Morave: Men 10 km sprint race highlights