The five-time Olympic champion won the final race of the season in Kontiolahti, FInland in a French 1-2-3, but Johannes Thingnes Boe was awarded the Crystal Globe after beating Fourcade by just 2 points.
On the women's side, Italy's Dorothea Wierer successfully defended her Crystal Globe title in another close-run finish with Tiril Eckhoff.
Fourcade, for many the greatest biathlete of all time, announced his retirement on March 13 2020 and two days later waved goodbye from the top of the podium where he's spent most of his career.
With the season cut short due to concern over the spread of coronavirus COVID-19, the 12.5km pursuit in Kontiolahti, Finland, suddenly became the final event of the season and it all came down to this one race.
"If there are tears, they are tears of joy." - Martin Fourcade
It looked like Fourcade's last dance would give way to yet another Johannes Thingnes Boe masterclass as the Norwegian took a big lead early on, but Fourcade and his French entourage overtook Boe to sweep the podium.
Boe would finish fourth on the day.
Tiredness played a big factor as the Norwegian slowed up, and when he missed three shots for the first time all season on his second-to-last shoot, Fourcade and the French trio closed in.
Fourcade, Fillion Maillet, and Emilien Jacquelin finished 1-2-3 with Boe in fourth.
Fourcade's 83rd World Cup win
The Frenchman's win in Kontiolahti means that he retures with 83 World Cup titles next to his name.
Yet another startling statistic for the athlete who has defined an era and become an icon in his discipline.
There wasn't the noise, or the send-off you would expect due to the fact that the event was held without fans.
But it was still an emotional moment for this French national hero.
"This was special for me today as everybody knows," said Fourcade afterwards, "it has been a dream for a bit more than 10 years."
"Of course I missed the fans," "he continued, "when I started back in the back in the Pyrenees mountains in France, it was no fans," referring to how far the sport has come since, with regular crowds of 10,000 people.
There was a sense of perfect symmetry to Fourcade's victory as he retires with a win exactly ten years to the day of his first ever win in an individual World Cup event, at the same course.
"I am proud I achieved what I did, proud I discovered myself along that journey and just a beautiful way to finish it." - Martin Fourcade
It's the end of a rivalry that has come to define biathlon in recent times.
And it was a classic encounter between the two, Fourcade coming out on top in Finland.
Afterwards Boe was told that one of the reasons that Fourcade has decided to retire is to give way to new champions like him, and Crystal Globe winner Boe was flattered:
"It's so amazing to hear such nice words from this biathlon legend. Martin pushed everyone here at the start line to be a better biathlete," he said.
"We have to just say a big thanks for everything he has taught us" - Boe thanks Fourcade
The 26-year-old Norwegian who already has 48 World Cup wins succeeds Fourcade as biathlon's biggest star.
The young gun noted how Norwegians will particularly miss the great rivalries with the French champion.
IBU World Cup Men's Biathlon Season 2019/2020 Results
The 2019/2020 season finished like this:
- Johannes Thingnes Boe 913
- Martin Fourcade 911
- Quentin Fillon Maillet 843
- Tarjei Boe 740
- Emilien Jacquelin 726
Dorothea Wierer retains women's Crystal globe 2019/2020
Italy's Dorothea Wierer retained her Crystal Globe title, holding off the challenge of Tiril Eckhoff.
Much like the men's race, it went down to the wire in Kontiolahti, with Eckhoff close enough before the final race to overtake Wierer who was wearing the yellow jersey.
But a disappointing shooting display ended Eckhoff's hopes as she missed six of her first ten shots.
In windy and difficult conditions Wierer also struggled, missing five of her shots, only marginally better.
It wasn't the finest display from either of the overall contenders, Eckhoff finishing 10th and Wierer 11th.
Wierer finished a second behind Eckhoff, but it wasn't enough to take the overall title away from the Italian.
France's Julia Simon completed an amazing day for the French team as she picked up her first ever win, Switzerland's Selina Gasparin was second and Italy's Lisa Vittozzi finished third.
Another legend retires
Finnish biathlete Kaisa Makarainen came in fourth in this home World Cup, and her tears at the finish line made it clear that this was the end of the road for her too.
The 37-year-old represented her country at three Olympic Games, won the 2011 World Championships and bows out with 85 podium finishes to her name.