The African nation was playing in soccer's biggest tournament for only the second time in their history after a 52-year absence.
Two second-half goals on Saturday (Sunday AEST) from Yoane Wissa and one from Fiston Mayele sealed the win and allowed Congo to join Cape Verde as another surprise qualifier for the round of 32.
Uzbekistan led through Eldor Shomurodov's first-half strike that looked set to end Congo's hopes.
But Sebastien Desabre's team, who had already pulled off one of the surprise results of the World Cup by holding Cristiano Ronaldo's Portugal to a 1-1 draw in their opening game, fought back after the break.
Trailing to Shomurodov's lobbed goal in the 10th minute, Congo equalised in the 68th when Wissa was brought down by Abdukodir Khusanov in the box for a penalty.
Wissa picked himself up and sent Uzbekistan goalkeeper Abduvohid Nematov the wrong way by rolling the ball into the bottom corner to spark a dramatic finale.
Mayele fired Congo ahead 10 minutes later when flicking past Nematov at the near post after Meschack Elia's shot was deflected.
Wissa put the result beyond doubt in added time with a curling shot into the bottom corner.
Congo's only previous appearance at the World Cup was when they competed as Zaire in 1974, losing all three games, including a 9-0 rout at the hands of Yugoslavia.
The draw against Portugal was their first point on this stage and they needed to follow that up with a first win to advance as one of the best third placed teams.
They became the eighth African nation to advance from the group stage at this tournament.
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