The 32-year-old was good after half the race but then crooked during the last part.
Halfvarsson finished 9.70 seconds behind the qualifying fastest skier, Alexander Terentev.
Six Swedish men stood on the starting line in the sprint qualifiers and all went on, except Halfvarsson.
Grate best Swedish
Best Swede in the qualifiers was Marcus Grate who came in seventh place.
Anton Persson, Gustaf Berglund and Johan Häggström also went on.