The result saw Ante Milicic's side finish runners-up of Group C behind Korea Republic, sending them through to the quarter-finals where they will face either Saudi Arabia or Tajikistan.
Western Sydney Wanderers' Oliver Puflett opened the scoring for the Young Socceroos in the 10th minute with a powerful volley at the end of Ben Folami's fine cross.
Jordan equalised in the second half through Omar Hani Al Zebdieh, but the Australians held on to the result that sealed their progress at the tournament.
Advancing to the semi-finals with a win on Monday will secure qualification to the U-20 World Cup held in Poland next year.
They would follow in the footsteps of the Joeys, who earlier this month sealed a place at the 2019 FIFA U-17 World Cup in Peru after reaching the semi-finals of the AFC U-16 Championship.
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