The 22-year-old who arrived in Sweden with 62 winners to her credit won the points-based competition which is staged over five legs with a total of 48 points from reigning champion, Sweden's Josefin Landgren on 43 points and Great Britain's Jane Elliott, standing in for Hayley Turner, back in third with 38.
After receiving her trophy from Svensk Galopp's Dennis Madsen, Fujita, who won two races and finished second in a third said, "It's unbelievable I am really happy. It is the first time I have ridden a winner outside of Japan. Travelling to Sweden and riding Swedish horses has been very good experience for me and I hope I can inspire other female riders. I am thankful to my trainer in Japan and my parents and to Svesnk Galopp for inviting me to Sweden."
Sophie Ralston representing Ireland and Great Britain's Georgia Cox finished fourth and fifth among the ten invited international riders with 34 and 31 points respectively.
There was a dramatic start to the Women Jockeys' World Cup for Cox when her Sunday morning flight from London Heathrow was cancelled forcing her re-route to Gatwick. She arrived just in time for the pre-racing photocall but after the time to way in for her first intended ride.
Two non-runners in the competitions' opening race, a 1200m contest created an opportunity for Jeane Alves de Lemos to pick up Cox's ride, Monkey Bar Flies, which finished third putting the Brazilian on the leader board with 10 points behind reigning champion, Sweden's Josefin Landgren who got her title defence off to the best possible start with victory aboard Paakame Enki and France's Alison Massin on Lushes Lashes.
Fujita took the second leg of the championship on Franciskus. However a second place in the 1400m contest for Josefin Landgren aboard Good Sensation maintained the Swede's position at the top of the leaderboard.
The third leg went to Ireland's Sophie Ralston who brought Mindbender into the winner's enclosure ahead of Iwannabetheonlyone and local rising star Ulrika Holmquist who rode four winners at the National Day meeting earlier this month, and Great Britain's Jane Elliott in third place on Haweswater.
Elliott came out best in a hard fought finish in leg four of the Women Jockeys' World Cup on Nastenka and her 15 points for victory added to placings in legs one and three elevated her to second with 34 points behind the reigning champion who picked up seven points for fourth, and only one point ahead of Japan's Nanako Fujita who finished second.
Fujita went into the final leg of the competition in third place but with just three points separating the first three on the leaderboard and sealed victory with a win aboard Chilterns ahead of Cox on Regan Budget chased home by Ralston and Jive Talkin.
Dennis Madsen, Svensk Gallop's Director of Racing said, "We are delighted for Nanako who helped us make the Women Jockeys' World Cup a truly international competition. The Women Jockeys' World Cup, and in particular, Japan's participation has generated a huge amount of interest in Swedish racing and we are grateful to all media, trainers, jockeys, owners and commercial partners who have supported the third running of this event at Bro Park."
Nanaka Fujita (JPN) 48 points
Josefin Landgren (SWE) 43 points
Jane Elliott (GB) 38 points
Sophie Ralston (IRE) 34 points
Georgia Cox (GBR) 31 points
Ulrika Holmquist (SWE) 28 points
Alison Massin (FR) 27 points
Jeane Alves (BRA) 25 points
Rebecca Danz (GER) 12 points
Kaia Sophie Ingolfsland (NOR) 10 points