The Welshman attacked with Zdenek Stybar (Etixx-Quick Step) and Peter Sagan (Tinkoff-Saxo) on the cobbled Oude Kwaremont climb and rode free from his two rivals in the final five kilometres. After winning stages and overall classifications, including the Volta ao Algarve in February, Thomas bagged his first international one-day win in an important spring campaign for Sky.
"It's a relief for him to win for the first time over here," Knaven told Cycling Weekly.
"He was close last year and the year before, always in a similar position, and now it looks like he's even better than in the years before.
"On these roads he's now one of the best, if not the best."
The E3 Harelbeke has a long list of winners in its 58 editions, but never a British rider before today.
Tom Boonen won the race a record five times. It used to be on Sunday, now Friday, but still comes around one week before the Tour of Flanders. With many of the same climbs and roads, it is considered a good indicator of who is on form before the biggest one-day race in Flanders.
"And of course, it's a big race in its own right. There's a big history here and it's a WorldTour race," Knaven added.
"All the big guys are here and they all want to win. If you can win this race then you can also win in the Tour of Flanders."
Thomas celebrated his hard-fought victory in the 215-kilometre race, which included Kwaremont beer for the winner in the press conference. As soon as the sun began to set on Harelbeke, talk turned to Ghent-Wevelgem on Sunday and the Tour of Flanders next Sunday.
"The guys are in good shape, they don't have to hold off on Sunday to be ready for Flanders, they still have a week to recover," explained Knaven.
"First we have to see how the weather is, how Viviani is, then anything can happen. What I saw Sunday, the weather doesn't look great, there will be a lot of wind, and probably not a 60-man group at the finish."
On week later, Thomas will be the clear leader for Sky heading into his biggest appointment this spring.
“Harelbeke is the final recital before Flanders,” said Knaven, “the last big practice and the win is a boost for his morale."
Thank you for reading 20 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1