Ustiugov, who won the Tour de Ski back in 2017, had picked up his first World Cup victory in a year in Lenzerheide three days after Christmas when he triumphed in the mass start 15km race.
The travel to Toblach did not change the form book though and the 27-year-old, who won the same event in Italy last year, took victory by more than 20 seconds.
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The former 30km world champion broke the back of the competition in the opening stages, gaining 15 bonus seconds by being the first over the opening checkpoint, and then clung on to seal victory.
WATCH: Ustiugov clinches second World Cup victory in a week
Rounding out the all-Russia top three behind him were van Yakimushkin and Alexander Bolshunov, who only secured third from Sweden's Calle Halfvarsson by 0.6 seconds.
It was a morning to forget for the Norwegians, who appeared to struggle to get their skis running freely in the conditions and only had one competitor in the top 20.
But it was a far better performance from Great Britain's Andrew Musgrave, who kept up his impressive Tour de Ski form by finishing 14th.
The 29-year-old from Poole, who finished on the podium in Toblach two years ago, remains on course for his best ever Tour de Ski result, sitting 17th in the standings.
In the women's 10km race, any waxing issues the Norwegians might have had seemed to have been left behind as they had four of the top five finishers.
Like Ustiugov, Therese Johaug went out hard to claim the 15 bonus seconds for being fastest over the first 1.7km and challenged the field to make it up on her.
Johaug was actually a tenth of a second down on teammate Ingvild Flugstad Oestberg with two kilometres to go but edged ahead in the closing stages to win by 0.7 seconds.
"I'm really happy and of course it was really tight," Johaug said.
"It was a hard race and I had to fight the whole way especially when I heard what the others were doing and I was really lucky to have someone just in front of me for the last 500 metres."
Stupak and Bolshunov lead the way in Engadin
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