The early energetic display would have pleased Iran coach Carlos Queiroz, who was restricted to a place in the stands after being sent off in the 1-0 win over South Korea last month.
However, Uzbekistan were defending bravely and with Asian Player of the Year Djeparov providing a series of dangerous set-pieces the visitors always looked a threat.
Queiroz introduced Karim Ansari at the break and he almost had an instant impact, but his steered shot from the edge of the area flashed just wide two minutes into the second half.
As the match wore on the technically superior visitors took control through midfield and grabbed the lead, inevitably from a Djeparov free-kick.
The much-traveled playmaker whipped in an inswinger with his left foot from close to the touchline which Bakaev poked home from close range with the Iran goalkeeper stuck on his line.
Iran pressed in the final stages and had the ball in the back of the net for a second time, but substitute Milad Nouri’s 91st-minute effort was ruled out again for offside.
The win gave Uzbekistan revenge for their 1-0 home loss to Iran in the opening match of the group in June which they had controlled throughout only to concede the winner in the 94th minute.