The dangerous Prince Tagoe scored twice while Saleh Bashar and Waleed Al Rajaa also netted for the hosts to secure the three points that ensured the Saudi side will finish top of Group D.
The defeat leaves Bunyodkor in second place in the standings and needing to avoid defeat in their final game against Al Shabab if they are to progress.
The visitors made a bright start to the game with Rivaldo twice heading over the bar as they looked to snatch an early lead.
But they found themselves behind in the 16th minute when Tagoe chased a fine ball over the defence, shrugged off the despairing challenge of a defender before wrong-footing the goalkeeper and slotting the ball into the net.
Bunyodkor again dominated possession as they searched for an equaliser and came close as Gochguly Gochguliyev headed into the side netting when unmarked at the far post while Anvar Gafurov also shot wide in the 36th minute.
Ettifaq punished the Uzbek side for those misses as Tagoe again found the net after Abdulrahman Al Qahtani cut the ball back for the Ghanaian, who smashed the ball home from six yards.
The game was over as a contest when Ettifaq added a third two minutes into the second half after Al Qahtani’s dangerous cross could only be pushed into the path of Bashar by goalkeeper Pavel Bugalo and the forward made no mistake from close range.
Bunyodkor offered nothing in the way of an attacking threat with Rivaldo and reigning AFC Player of the Year Server Djeparov both well marked by the Ettifaq defence.
Ramos’s cross sailed harmlessly over the bar while Djeparov launched an effort from a decent position high and wide.
Ettifaq had visibly taken their foot off the pedal although substitute Salah Aqqal had Bugalo scrambling with a long-range effort in the 75th minute.
Bunyodkor were then denied a goal when Jamaan Al Jamaan superbly headed off the line but they fell further behind in the 81st minute when Al Rajaa drove the ball home following a well-worked move free-kick.
That proved to be the last chance of note as Ettifaq preserved their clean sheet whilst ensuring their place in the last 16.