The 26-year-old, whose international career has been limited by injury, is likely to sit out Australia's remaining three Pool C matches at least, starting with Saturday's clash against the Irish in Auckland.
The Queensland Reds flyer has been in sparkling form this season and was installed as the bookmakers' favourite to finish the tournament as the highest try-scorer.
Ioane opened his account with Australia's fourth try in the 32-6 win over Italy but injured his thumb soon after when he made contact with the boot of Italian winger Mirco Bergamasco. The fracture was confirmed after a scan on Monday.
"Ioane will be operated on and will remain with the Wallabies in New Zealand," said a team statement.
"He is expected to be available to play again later in the tournament although the exact timelines on when he might be able to return will not be known until after the joint has been operated on, and his rehabilitation from the injury has begun."
Players can be replaced in the 30-man World Cup squads on medical or compassionate grounds but the replacement must be permanent.
The versatility of the Australian backs will help fill the void left by Ioane.
James O'Connor played a key role in the victory after coming on from the replacements' bench in Albany, while Drew Mitchell, who scored seven of his 26 international tries at the 2007 World Cup, has recovered from a nasty ankle injury.
Adam Ashley-Cooper, normally a centre, started the Italy match on the wing and can play across the back three, while fullback Kurtley Beale made his international debut out wide.
Wallabies coaching coordinator David Nucifora told reporters earlier on Monday that Ioane's injury was the only major concern after the often bruising encounter with the Italians.