The Millennium Stadium match falls outside the November international window and Stade Francais were therefore under no obligation to let Genia play for his country.
According to a report in Sydney's Daily Telegraph, Australia coach Michael Cheika had requested Genia be released but was turned down by the Top 14 club.
Genia will be available for the tests against Scotland, Ireland and France inside the international window, but negotiations are likely to begin anew ahead of the match against England on December 4.
Cheika, who was coach of Stade Francais from 2010-12, sent the scrumhalf back to France before the test against the All Blacks last month in the hope of building some goodwill.
The French club would not have anticipated having to release Genia for international duty at all when they signed him, given he would have been ineligible until Cheika orchestrated the "Giteau Rule".
With 72 Wallabies caps, Genia comfortably qualifies to play for his country under that rule, despite playing his club rugby outside Australia.
Nick Phipps is almost certain to deputise for Genia on Saturday, as he did against the All Blacks last month, as Australia bid for a 12th straight win over the Welsh to kick off their bid for a first Grand Slam since 1984.
