A picture of the 35-year-old defender was posted on the J.League club's website (www.ardija.co.jp) on Sunday, though no details were provided on the length of his contract with the side based in the northern suburbs of Tokyo.
The Socceroos captain, who has also played for English Premier League clubs Everton and Blackburn Rovers, and Turkish side Galatasaray, led the country's successful qualifying campaign for the 2014 World Cup finals in June.
However, head coach Holger Osieck had urged Neill to find a club soon to help him retain his spot in the national team for next year's prestigious event in Brazil.
Omiya have recently struggled for form, losing their last six matches and slumping to fifth spot in the J.League, a run that led to the sacking of Slovenian coach Zdenko Verdenik.
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