Boonen went down hard early in the race, before the La Houppe climb. He managed to finish 11th behind winner Peter Sagan (Cannondale) but admitted it had been a painful day in the saddle and on the cobbles.
Omega Pharma-Quick Step has already lost Mark Cavendish after the Manxman was hit by a fever but Boonen confirmed he would ride on Sunday after medical staff taped his thumb and he tested how it felt during Saturday's training ride.
"The medical staff taped his thumb this morning, and Boonen was able to go out for a ride with the rest of the team on Saturday, even with some soreness," the Omega Pharma-Quick Step team said in a statement.
"Tom Boonen will be at the start at Gent-Wevelgem. If it will be necessary after the race, Boonen will pass further examinations.
"Boonen suffered a strong contusion on his right thumb that caused him pain on the articulation. The thumb is swollen and he also has a stretched ligament."
With the Tour of Flanders just a week away, Boonen tried to stay optimistic after fighting the pain to finish E3 Harelbeke.
"It’s never good to ride over the cobbles when your hand hurts. I did 100km with a lot of pain. On the climbs there’s often a gutter so that was fine but on the cobbles it hurts a lot," Boonen said.
"I managed to finish the race so I’m not panicking. Most of the times they’re able to do something with these kind of injuries but it’ll hurt a lot. It’s a bit swollen. It will probably be alright."
lljo Keisse will replace Cavendish in the line-up for Gent-Wevelgem and Matteo Trentin also returns to competition after missing E3 Harelbeke due to gastroenteritis.
Also riding are Zdenek Stybar, Gert Steegmans, Martin Velits, Nikolas Maes and Stijn Vandenbergh.