The Lotto-Soudal rider dropped Wout van Aert and Romain Bardet with 12km to go, and the pair had no answer allowing Benoot to cross the line in Siena del Campo unchallenged.
Bardet claimed second while Van Aert had to settle for third place.
The race was run in exceptionally muddy conditions, as melting snow and further rain churned up the race's famous unpaved sections.
The mud appeared to favour Van Aert, a three-times cyclo-cross world champion, but it was the 23-year-old Belgian Benoot who proved the strongest.
Anna van der Breggen won the women's race thanks to a brilliant solo effort, with Katarzyna Newiadoma and Longo Borghini joining her on the podium.