After sweeping the podium in Saturday's skiathlon, Norway took the top three places again with Erik Valnes claiming silver, 8.8 seconds behind Klaebo's winning time of 28 minutes 16.6 seconds and Harald Oestberg Amundsen the bronze.
Nyenget looked in position to claim a podium spot but went tumbling at the turn on the top of the final climb to ruin his chances.
The 108 contestants in the men's race had to cope with difficult weather conditions, with the striding classic technique made much more difficult by build-ups of loose, heavy snow in the carefully-prepared tracks.
With the racers starting at 30-second intervals, Klaebo, who claimed his first world championship gold in an individual distance race on Saturday, started well before taking over at the mid-point of the race.
His powerful skiing over the second half of the course ignited the home crowd of over 15,000 as he passed the final split time at 9.2km in the lead, and the 28-year-old thundered to the end of the course to win his 12th world gold medal.