Alex Howes will replace Vanmarcke in the team's roster, Garmin-Barracuda's Allan Peiper confirmed to Cyclingnews.
"Sep crashed in Denain in the second last lap and landed on his knee. He made it back to the peloton but he will need some days off to recover and we want him to focus on that," Peiper said.
"We have added Alex Howes to the roster, who finished a fine 6th in the Brabantse Pijl yesterday. We still have a strong team for Amstel with Dan Martin and Ryder Hesjedal along with Johan Vansummeren coming off a strong ride in Paris-Roubaix, Fabian Wegmann and the Dutch riders Thomas Dekker and the Kreder brothers."
Vanmarcke has been Garmin-Barracuda's revelation this spring. The 23-year-old Belgian confirmed his promise to the world when he out-sprinted Tom Boonen (Omega Pharma-Quickstep) and Juan Antonio Flecha (Sky) to win the Omloop Het Nieuwsblad.
Vanmarcke previously placed second in Gent-Wevelgem in 2010, and last year narrowly missed the podium in the E3 Prijs Vlaanderen - Harelbeke, placing fourth. He was fifth in this year's edition.