The hosts took the lead with less than 10 minutes on the clock through Majed Al Marshadi before Christian Wilhelmsson added a second in the 57th minute.
That goal clearly knocked Bunyodkor for six after they had looked like potentially getting back into the game and the result was put beyond a doubt when Thiago Neves got a third for Al Hilal after 61 minutes.
It brings to an end a disappointing AFC Champions League campaign for Bunyodkor, who had reached the semi-finals in 2008 and the quarter-finals last year.
The Uzbeks were immediately on the back foot from the start and found themselves a goal down with just eight minutes gone when Thiago Neves lofted a ball into the area and Al Marshadi rose highest to direct a header into the back of the net.
That goal stunned the Uzbeks and Al Hilal enjoyed a spell of pressure, coming close to adding a second soon after when Mohammed Al Shalhoub fed a pass for Yasser Al Qahtani but the striker lashed his shot high and wide.
A second goal for Al Hilal seemed imminent and Al Marshadi had his shot cleared off the line by a defender after 19 minutes.
Bunyodkor finally mustered their first chance of note in the 30th minute when Rivaldo released Anvarjon Soliev and the forward charged down on goal only to scuff his shot harmlessly at the goalkeeper.
Their failure to find a first-half equaliser proved costly as Al Hilal extended their lead in the 65th minute when a swift counter attack saw Al Shalhoub play the ball into the path of Wilhelmsson and the Swedish winger drove an angled shot into the inside of the let upright.
Wilhelmsson then turned provider as Al Hilal ended all hope of Bunyodkor reaching the last eight when his pass sent Thiago Neves through on goal and the Brazilian coolly lifted the ball over the goalkeeper and into the back of the net.
Bunyodkor attempted to rally soon after when Victor Karpenko’s close-range volley beat the keeper but struck the inside of the post before the defence cleared the danger but that was as close as they came to scoring as Al Hilal comfortably closed out the remainder of the game.