The Danish rider, signed from NTT Pro Cycling, managed to finish the opening stage on Thursday in 127th place. However, scans later revealed fractures to the second and third metacarpals in his left hand.
Valgren will undergo surgery on Thursday.
"It’s not the best start, but it can only get better from now on," Valgren said.
"It was great to race with the guys, even though it was only for one day, I really enjoyed the atmosphere and I know it will be a nice week."
EF Education-Nippo stated that a timeline for Valgren's racing return will be decided following his surgery.
The so-called Opening Weekend of Omloop Het Nieuwsblad and Kuurne-Brussel-Kuurne was likely to have been on his original programme at the end of February, as he came in to bolster EF's Classics department.
Valgren is a former winner of the Omloop, as well as Amstel Gold Race, and has already spoken of his desire to target the Tour of Flanders alongside 2019 winner Alberto Bettiol. Sep Vanmarcke, the team's previous Classics captain, has moved to Israel Start-Up Nation for this season.
EF continue in the four-day Étoile de Bessèges with Bettiol, who won the final time trial last year, along with fellow Classics riders Jens Keukeleire, Sebastian Langeveld, Jonas Rutsch, and Julius van den Berg. The line-up is completed by Grand Tour leader Rigoberto Urán.
The opening stage of the race was won by Cofidis' Christophe Laporte in an uphill sprint. Thursday's stage 2 is a largely flat 154.1km route based in Nîmes and should see the sprinters contesting the spoils.
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