Socceroos coach Ange Postecoglou said Tuesday the 36-year-old defender will not be on the 30-man preliminary roster to be announced next week.
Neill made his Australia debut in 1996 and has 96 international appearances. He captained the team for the first time in 2006 and was part of the Socceroos at the 2006 and 2010 World Cups.
After playing for Millwall, Blackburn and West Ham, Neill is on loan from Watford to Doncaster Rovers.
"In the end I just had to make a decision, not so much about the recent history but the last six months, in terms of form and fitness," Postecoglou said. "There just wasn't enough evidence there for me to say he'd be able to hold up in a World Cup. It was both a combination of the lack of regular football and the little niggles he got that made the decision for me."
Postecoglou took over as coach in October when Holger Osieck was fired after consecutive 6-0 exhibition losses to Brazil and France. Postecoglou wanted to tell Neill before the roster is announced
"It was difficult," Postecoglou said. "He's worked damn hard to get himself ready and available; he's shown an enormous determination to go to this World Cup."
Australia is in Group B in Brazil with defending champion Spain, 2010 finalist Netherlands and Chile.