Following the ski jumping element of the Individual Gundersen Large Hill/10.0km event, Japan's Watabe led the way – giving him a nine-second advantage over nearest challenger Jens Luraas Oftebro heading into the 10km cross-country.
Martin Fritz was in third – with a 44-second deficit to the leader – while Nordic Combined's dominant force and this season's Crystal Globe winner Jarl Magnus Riiber was down in 16th, 1:40mins behind Watabe.
That ultimately proved too much for superstar Norwegian to overcome, as he finished in tenth place – just the third race of 16 this season that he hasn't won.
Watabe made the most of his jumping performance as he and Oftebro formed a two-man group in the cross-country that protected their advantage over the rest of the field.
The Japanese skier then pulled away from the Norwegian in the final stages to cross the line in a winning time of 25:41.1mins – his first World Cup win since he triumphed in Schonach back in March 2018.
Talented oungster Oftebro appeared to have nothing left as he was also overhauled by two other skiers to agonisingly miss out on a podium spot as he came fourth.
Another Norwegian, Joergen Graabak, ultimately took silver, just 2.9seconds behind the winner, with Germany's Vinzenz Geiger grabbing bronze.