The 27-year-old Norwegian defended his lead in the general standings from his teammate Sturla Holm Laegreid, who was just four points behind ahead of the 15km men's mass start, the last event of the season, in Oestersund, Sweden.
Boe cleared 17 targets out of 20 and finished third, 17.5 seconds behind winner Simon Desthieux from France, while 24-year-old Laegreid ended with four misses and had to settle for eighth, over 44 seconds off the pace.
PyeongChang2018 gold medallist Boe ended the season with four wins, six less than last season, but that was enough to top the overall rankings with1,052 point ahead of Laegreid with 1039.
"I have no words to describe how relieved and how happy I am," Boe told IBU TV after the race.
"Every title has his own story, Sturla (Holm Laegreid) put up such a good fight for me, he really pushed me to my limits and he's shown that it's possible to do such great shooting every time.
"I have a big motivation to train with him next season and hopefully we're going to help each other to maintain the same level."
First World Cup win for Tandrevold
Previously in the women's 12.5km mass start, Ingrid Landmark Tandrevold of Norway won the last event of the season to clinch the discipline's crystal ball.
In an event affected by strong winds, the 24-year-old hit 15/20 from the shooting range and finished 7 seconds ahead of Dzinara Alimbekava of Belarus, with Franziska Preuss of Germany in third.
It was the first World Cup individual win for Tandrevold, who won silver in the mass start event at the 2021 World Championships in Pokljuka, Slovania.
She also became the third Norwegian woman to win the mass start title after Live Grete Poiree in 2004 and Tora Berger in 2013.
Overall crystal globe winner Tiril Eckhoff finished seventh in today's race ending with 1,152 points in the general standings, ahead of teammate Marte Olsbu Roeiseland (963) and Preuss (840).
"It's a little bit emotional, I'm super happy, it's been quite a journey," said Eckhoff, who missed last year's title by just 7 points to Italy's Dorothea Wierer.
"I think that's something with me, I never give up, I have the will to do the boring stuff and the training, I always do a little bit more.
"I'm just proud, I didn't believe it would be happen because it was so hard last year, I'm so happy."