The Welshman – winner of E3 Harelbeke and third in Ghent-Wevelgem – fell short due to tactics and strength. He was marked by a rival team and lacked energy when he reached the final Paterberg climb.
"It's mainly tiredness, but obviously I'm gutted, as well," Thomas explained after a shower at the team bus.
"I was in good shape and was hoping for more, it's just down to the legs. I lacked that five per cent that I had last week."
Last week in E3 Harelbeke, Thomas helped form a three-man move on the Kwaremont climb and then rode clear from rivals Peter Sagan and Zdenek Stybar with 4.3 kilometres remaining.
He finished third two days later in Ghent-Wevelgem.
Man of the moment Alexander Kristoff out-paced fellow escapee Niki Terpstra to take the victory in the 2015 Tour of
Today in Flanders, he attacked on the same Kwaremont climb at 17 kilometres out and again had Stybar for company. This time, however, Stybar's Etixx team-mate Niki Terpstra was further up the narrow lanes with eventual winner, Norwegian Alexander Kristoff (Katusha). Stybar refused to help Thomas pull closer to his team-mate and the move quickly petered out.
"Initially when I went, I felt okay, but when you know that he's sitting on you... In the flat part, I sort of eased up a bit, then everyone sort of came up," Thomas added.
"On the Paterberg, I just lacked that last bit over the top, that's when Sagan and [Greg] Van Avermaet went.”
Thomas remained in a group of about 15 riders chasing two duos: Kristoff and Terpstra, and Sagan and Van Avermaet. Their advantage grew, shrank and grew again.
“Once you are stuck in that group behind, it's hard to get a gap especially when a couple of guys attack and everyone follows. Especially for me, not really having that massive kick.
"I just lacked that punch that I had last week on the Kwaremont. I had to have a go, the boys rode all day for me. It was just not enjoyable, no one would work together, just a typical big race with big leaders and no one wanting to go work."
Sky rode at the front for many of the 264 kilometres between Bruges and Oudenaarde. Elia Viviani, Salvatore Puccio and Christian Knees worked before Bradley Wiggins, Bernhard Eisel, Ian Stannard and Luke Rowe took over.
Wiggins' crash, however, caused a stir. In a left corner with 152 kilometres to race, a rider slipped in front of Wiggins and caused the incident. Wiggins jumped back up, wobbled and climbed on a new bike. He later switched bikes again and returned to the head of the group to pull for Thomas again.
"When he came back, he celebrated. It took him about 50 kilometres to get to the front. That was different, I’ve never seen someone get to the front, go one-handed and cheer for getting there," Thomas added.
"Everyone just committed. I couldn't have asked for more, the boys rode good, it's just a shame I couldn't get a result."
Thank you for reading 5 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