The British and Irish Lions fullback was hurt midway through the first half of Cardiff's United Rugby Championship victory over Munster on Saturday.
He has undergone surgery and faces a recovery period of 12-16 weeks, his club said.
Wales are scheduled to face Australia, New Zealand, Argentina and Georgia in November.
Williams, who has won 81 caps, also offers Wales head coach Wayne Pivac an option on the wing.
Johnny McNicholl and Leigh Halfpenny would be likely full-back candidates when Wales continue their World Cup countdown.
Halfpenny has not played for 14 months due to a serious knee injury, but he is understood to be closing in on a comeback for the Scarlets.
Cardiff said: "Liam Williams underwent surgery last night after suffering a collarbone injury.
"The Wales and British and Irish Lions full-back had impressed on his Cardiff debut before damaging his shoulder in a tackle on the 20-minute mark.
"Williams now faces a recovery period of 12-16 weeks on the sidelines following surgery."
The 31-year-old made his Test debut in 2012, and has featured for Wales in their last two World Cup campaigns.
9°C