The Scarlets tight-head, 23, suffered a ruptured pectoral muscle at a Wales training camp and will undergo surgery, ruling him out for 12 to 16 weeks.Cardiff Blues prop Scott Andrews has been called into the squad that will travel to Doha, Qatar, this weekend.
“It is hugely disappointing for Rhodri,” said Wales coach Warren Gatland.
“He was working extremely hard out in Switzerland. We wish him all the best with his recovery from the injury.
“It is a great opportunity for Scott to come into the squad and show us what he is capable of.
“In terms of the tight-head position, Samson [Lee] has continued to make excellent progress and we have been very impressed with both Aaron Jarvis and Tomas Francis during the first batch of training.”
Jones, who has won 13 Wales caps, missed the 2015 Six Nations after dislocating a shoulder in January.
Wales’ first-choice tight-head Samson Lee is currently recovering from a serious Achilles problem suffered during the Six Nations.
Centre Jonathan Davies has already been sidelined from the World Cup due to injury, while full-back or wing Liam Williams is still recovering following surgery on an injured foot.
After warm-up Tests against Ireland, home and away, and Italy, Wales begin their World Cup campaign against Uruguay on 20 September in Cardiff.
Gatland’s side also face hosts England, Australia and Fiji in Group A.