The Norwegian crossed the line in 39:32.7 to make it a hat-trick of wins in the Czech Republic after anchoring his country's relay win and claiming Friday's 10km sprint.
The 26-year-old stormed to victory in the last loop despite picking up three penalties, with France's Emilien Jacquelin his nearest rival after shooting clean to finish second 15.1 seconds behind.
Arnd Peiffer of Germany completed the podium places, finishing 25s back, while Dmytro Pidruchnyi of the Ukraine and Boe's teammate Erlend Bjoentegaard were fourth and fifth.
But it was another very good day for Boe, who closed the gap on France's Martin Fourcade at the top of the overall World Cup standings to 43 points.
"I found out in the first downhill that I had two metres on the field; I knew I had good skis," he said. "We had very good skis here all weekend. I am in good shape so I put in high speed from the start.
"I think that is why I was missing something in the shooting range. I managed to hit five in the last standing. It was a hard fight with Jacquelin. I am very happy with my win and my teammates."