Frenchman Fourcade was able to limit the damage as he came second in the 10km race in Kontiolahti, securing the small crystal globe as the winner of a slightly truncated sprint season.
Boe's time of 22:27.8mins was 21.1 seconds better than Fourcade, who finished one second ahead of compatriot Emilien Jacquelin, with the top five skiers all shooting clean.
This victory gives the 26-year-old Norwegian defending champion one last chance to defend his title on Saturday, in the 12.5km pursuit, the last event of the World Cup, now that next week's meet in Oslo has been cancelled due to coronavirus.
"I felt the pressure from the start," Boe admitted. "But I was relaxed and quite confident by the time I started to shoot."
"I'm in a big fight for the World Cup but I have to treat it as normal and take it one race at a time."