The Swede finished fifth in the heat and therefore there was no possibility of advancing on time for Anger.
World Cup leader Johannes Høsflot Klæbo won the semifinal ahead of his compatriot Erik Valnes. Anger finished fifth and was 57 hundredths behind fourth-placed Jules Chappaz, France, who along with third-placed Oskar Opstad Vike advanced on time.
Anger's time in the semifinal was over two seconds faster than Norwegian Even Northug's winning time in the other semifinal.
It wasn't what I wanted with the day. I go for it and think it's going to be a fast and good heat, but I don't get the pace with me and they come with better pace behind. Tough, says Anger.
It's just to recharge and come back with a vengeance tomorrow, but it's sour, he continues.
Anger was the only Swedish skier in the semifinal. The qualified World Championship skiers Marcus Grate and Oskar Svensson were eliminated already in the qualifying round.
There's nothing worse in this sport than being eliminated in the qualifying round when you know you're capable of being on the podium. It's something that doesn't add up with the prologue this year for me, says Grate, fresh SM winner and World Cup third in the last sprint event on Tour de Ski, to Viaplay.
Edvin Anger had the third fastest time in the qualifying round and then won his quarterfinal before the day ended in the semifinal.
Klæbo won the final ahead of his compatriots Valnes and Opstad Vike.
