Essa Obaid gave the home side the lead after only three minutes and Zimbabwean striker Musawekosi Mguni added a second six minutes before the break as Al Shabab registered their first win of the competition.
The home side were looking to bounce back from last week’s dismal 2-0 defeat to Sepahan in Iran and could not have asked for a better start as they raced into a quick lead.
Attempting to reach to a long pass, Mguni slammed into Bunyodkor goalkeeper Pavel Bugalo and the ball squirted loose to Obaid who tucked it away into the empty net.
Stunned by the early setback, Bunyodkor gradually came back into the game and threatened to equalise midway through the first half as Brazilian midfielder Victor Joao and Anvarjon Soliev both shot wide.
Al Shabab responded with Brazilian midfielder Carlos Renato firing in a powerful long-range effort that Bugalo turned aside at full stretch.
On the half-hour mark, the Uzbek side were awarded a free kick on the edge of the area and former FIFA World Player of the Year Rivaldo stepped up to curl in a shot that slammed against the woodwork.
Bunyodkor continued to apply the pressure and should have levelled the score in the 36th minute when Server Djeparov reached a loose ball and fired in a shot which was well saved by Al Shabab goalkeeper Ismail Rabee.
The visitors would pay for their profligacy as Al Shabab extended their lead in the 39th minute.
Essa Mohamad sent in a long ball from the middle of the pitch which was met by Mguni, who outjumped the Bunyodkor defence to send a looping header past the advancing Bugalo.
Mguni should have netted his second of the night in the first minute of stoppage time when he cut into the box from the left flank but shot wide.
Al Shabab controlled proceedings in the second half and went close to adding a third goal six minutes after the hour when Carlos Renato’s shot from outside the box went just past the left upright.
Bunyodkor were unable to create any clear-cut chances and were fortunate not to concede again as substitute striker Salem Saad shot over after a quick counter-attack.