The Syria match is Australia's final Group B match at the tournament, with the Socceroos needing a win or draw to ensure progression.
Centre-back Sainsbury's consecutive yellow cards against Jordan and Palestine earned him a one-match suspension and forced coach Graham Arnold into a reshuffle.
Despite strong showings in midfield, Milligan moves to centre-back where he has played many times before, and Luongo starts in the three-man midfield - partnering Jackson Irvine behind Tom Rogic.
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