In the middle of the half race after 14.9 km, Dygert, who started last, led by 26 seconds ahead of the Swiss Marlen Reusser.
In a right turn, she got several throws on the bike and could not straighten it but flew handcuffed over the railing and did not reach the goal on the Formula 1 track Imola.
Due to the corona pandemic, the tempo WC was Dygert's season debut.
Lisa Nordén was 14th last year and was in 14th place halfway but lost towards the goal and finished 24th.
Mechanical problems were behind that loss.
- I got a chain jump and unfortunately lost a lot of time there.
It was aggressively the last bit when I would press, it might be too much.
It felt as if oceans of time passed by, a couple of seconds can make several placements, says Nordén to SVT Sport.
The penultimate starter Anna van der Breggen won the race after passing Marlen Reusser with a strong finish.
van der Breggen was completely finished and had to be helped up after the first World Cup gold in pace - after four silvers.
Annemiek van Vleuten gave up the line race after the wrist injury in Giro Rosa last week but hopes to be able to defend her world champion jersey in the line race on Saturday.