William Poromaa was in the tight group for a long time but lost after the change of skis when three Norwegians pulled away.
Then the 22-year-old fought against Pål Golberg for fourth place but had to give in to a sprint duel and finished fifth, just over 30 seconds off the podium.
After the finish, Poromaa was disappointed and went into the sideline but got up unscathed.
In his first WC two years ago, Poromaa finished ninth in the skiathlon and in Planica the Swede was chasing a medal but failed to reach the podium.
It was an all-Norwegian podium where Simen Hegstad Krüger won before Johannes Hösflot Kläbo and third was Sjur Röthe.
Calle Halfvarsson, who finished fifth in Thursday's sprint, was sixth, while Jens Burman finished eleventh.
The Swedish duo was at the top during the first half of the race, but when the Norwegians increased the pace, they had to give up.
The text is updated.