The 33-year-old came 10th with a cautious run in Switzerland to climb above injured Norwegian Aksel Lund Svindal in the 2015-16 competition.
Svindal, who was absent after a knee operation following a crash in Kitzbuehel in January, finished second in the standings ahead of Fill's compatriot Dominik Paris in third.
Meanwhile in the women's downhill, Swiss skier Fabienne Suter climbed into second place in the standings with a runner-up spot behind Wednesday's race winner Mirjam Puchner of Austria.
Lindsey Vonn had already wrapped up her eighth World Cup downhill title in February before ending her season
due to a fractured knee.
Heading into World Cup finals week in St. Moritz, Fill was tied for the lead on 436 points with Svindal and one of five skiers who could win the title, alongside Paris, Norway's defending champion Kjetil Jansrud and France's Adrien Theaux.
As the final racer down in cloudy conditions, Fill was well off the pace of winner Beat Feuz of Switzerland and unsure in the finish area whether he had done enough to clinch the title.
After a few moments he was informed he had won his first Crystal Globe, and began celebrating.
"It is a great feeling and a dream come true for me," said Fill. "It was not an easy race for me as the last racer, the visibility wasn't good and conditions were hard, but in the end it was a perfect day."
Fill's season total of 462 points was 26 ahead of Svindal and 30 in front of Paris.
Jansrud was fourth on Wednesday and also ended the season on 432 points, but with only one race win he was edged on countback by Paris -- who clinched back-to-back downhill victories ahead of the finale.
American Steve Nyman finished 0.08 seconds behind Feuz, with Canada's Erik Guay third. Theaux and Paris failed to score any points, finishing 16th and 19th respectively.
Puchner landed her maiden podium place by 0.13 seconds from Suter and Italy's Elena Curtoni, with Switzerland's Lara Gut 13th to extend her unassailable lead in the overall standings.
Canada's Larisa Yurkiw finished third in the downhill standings after placing 17th.
"It's a good way to end the season," Suter told the FIS official website. "The podium was a good finish for me and now I can look ahead with full motivation for next season."
Vonn, who was in St. Moritz to pick up her 20th career World Cup title, said: "It's a little bittersweet for me.
"Naturally I'm really happy to win the globe, but to watch as a spectator and not race is really hard."
Vonn won five downhills this season to take her overall World Cup tally to 76 victories as she chases Ingemar Stenmark's record of 86.
But the American, 31, took the decision to end her season after scans revealed three knee fractures following a crash in Andorra.
"If this year had been an Olympic year I probably would have taken the risk, but I'm looking forward to the next two years and I really want to be able to walk when I'm older," she told Eurosport.
"I'm definitely not quitting anytime soon. I have a lot left to do in the sport. I'm having fun and I love what I do."