Hussein headed the Lions of Mesopotamia into an early lead in Qatar's Schooling City Arena after Japan guardian Zion Suzuki neglected to manage a cross.
And he doubled their lead just before Half-time with another header, this time from Ahmed Al-Hajjaj's cross.
Japan's goal came in Injury time at the end of the game, Liverpool's Wataru Endo heading in.
This was whenever the Samurai first blue, ranked 17th in the world, had lost to Iraq, ranked 63rd, in 42 years - a run of nine games.
The team led by Hajime Moriyasu, which defeated Vietnam 4-2 in the opening game, may need to win their final match against Indonesia to advance to the next round.
Iraq, who beat Indonesia last time out, can afford to rest Players against Vietnam.
The top two automatically Qualify, with the four best third-placed teams also progressing to the last 16.
Hosts Qatar and Australia were the first two teams to seal their places in the knockout stages.
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