Watabe had climbed the World Cup podium individually three times this season but a win was proving elusive with the 23-year-old finishing the first event in Italy in fifth.
However it was to finally be his day on Sunday as he dominated the ski jump and then the cross-country ski – even affording himself a celebration before completing the win.
Watabe of Japan was the only athlete in the field to break the 130 metre barrier in the ski jump – recording a distance of 133.5m for an overall total of 138.2 and 20-second cushion.
However Watabe hardly needed the extra 20 seconds in the cross-country ski as he stormed away and built a huge lead before easing off to record a time of 28:27.8 minutes.
The Japanese athlete celebrated well before the line and, despite his rivals closing as he took his foot off the pedal, he knew it wouldn’t cost him a much-deserved win.
Norway’s Mikko Kokslien was the best of the rest taking silver just three seconds behind Watabe for his third podium finish in Italy after a bronze in the first event and gold in the team sprint.
American Bill Demong completed the top three, finishing nearly a further second back but well ahead of German trio Johannes Rydzek, Eric Frenzel and Tino Edelmann.
France’s Jason Lamy Chappuis, who was eighth, still has a healthy lead at the top of the World Cup rankings with 888 points but Watabe has moved into third – one point behind Alessandro Pittin.