The Welshman's withdrawal means neither he nor Tour de France winner Chris Froome will compete in the USA.
Froome broke a foot in a crash at the Vuelta a Espana, ruling him out.
"It's been a hard decision to make but the season has taken its toll on me and I don't feel physically up for a good Worlds," Thomas, 29, wrote on Facebook.
"I don't want to go there just to make up the numbers, I'd want to be competitive or at least do a good job for the boys."
Thomas says he wants to rest ahead of 2016 when he feels a top-five Tour de France spot is possible along with an Olympic track medal.
"I love racing for GB and the Worlds are a really special race so it was a difficult decision to make, along with the team, but I feel it's best to rest up now before it's all systems go for a big year next year."
Fellow Briton Mark Cavendish crashed out of the Tour of Britain last week and suffered a shoulder injury, but is hopeful of competing in Virginia as the men's road race takes place on the final day of the championships - 27 September.
Geraint Thomas has pulled out of the UCI World Road Race Championships in Virginia from 19-27 September, saying he does not feel "physically" up to it.