Edmondson won the race in a two-up sprint over Italian Gianni Moscon in Oudenaarde after a challenging 177km.
Three Australians - Edmondson, Miles Scotson and Alex Clements - made the select 40 rider group over the Eikenberg.
Over the Koppenberg Edmondson was part of a nine rider group that would further split to just Edmondson, Moscon and Truls Engen Korsaeth (Norway).
With seven kilometres remaining Edmondson and Moscon had distanced Korsaeth and had a 40 second advantage. Edmondson was able to hold off Moscon for the victory, the biggest of his road career.
Korsaeth finished seven seconds behind the pair, with
more than a third of the field failing to finish the cobbled race.
Under 23 Ronde van Vlaanderen: 177km, Oudenaarde
1 Alex Edmondson (AUS) 4hr 29min 4sec
2 Gianni Moscon (ITA)
3 Truls Korsaeth (NOR) Team Joker 0:00:07
4 Nans Peters (FRA) 0:00:54
5 Franck Bonnamour (FRA)
6 Mihkel Raim (EST) 0:01:23
7 Anders Skaarseth (NOR) Team Joker
8 Franck Grelier (FRA) 0:01:37
9 Mads Pederson (DEN) Cult Energy 0:01:39
10 Owain Doull (GBR) Team Wiggins