United Arab Emirates won Group B with seven points from three matches and the Uzbeks, on five points, followed it into the quarter-finals ahead of Paul Okon's Australians on goal difference.
The Young Socceroos' failure to survive the group phase also means they will not qualify for next year's under-20 FIFA World Cup in New Zealand.
Top spot in the group was at stake at the Youth Training Centre in Yangoon and both teams started brightly in a brisk opening to the match.
Goalkeeper Jordan Thurtell was forced to come out of his charge to block the advance of striker Eldor Shomurodov, who was clean through.
Despite both teams' attacking intent, scoring chances were few and far between and there was no score at halftime.
With United Arab Emirates two goals up against Indonesia at halftime in the other group match, the Australians had to go for a win to stay in the tournament.
They duly got the goal they were after in the 65th minute but the Uzbeks drew level 15 minutes later.