Zaynitdin Tadjiyev headed in the opener seven minutes before half-time and substitute Alexander Geynrikh sealed the three points by blasting home 12 minutes into the second half.
It was the fourth win in five games for the Tashkent side, who moved up to 13 points, two clear of second-placed Al Hilal with one game remaining.
A draw with the Saudi side in Riyadh in a fortnight will see them secure first place and a home match in the round of 16.
With Al Ahli out of contention after managing only one point, coach Ivan Hasek rang the changes in his line-up which included only two players who started the 2-1 home loss to Pakhtakor in March.
The home side made much of the early running and could have gone in front after four minutes when a cross from the right by Ilhomjon Suyunov found Farhod Tadjiyev, whose diving header flew narrowly wide.
Tadjiyev surged down the left channel in the 22nd minute only to be denied by goalkeeper Said Yousuf at the near post.
The resulting corner was directed on target by Darko Markovic but Yousuf stopped the ball on the goal line with help from defender Ali Hussain.
Al Ahli rarely threatened but nearly took the lead in the 25th minute when Salem Khamis unleashed a shot from 25 metres that was brilliantly palmed away by Ignatiy Nesterov as it curled towards the top corner of the Pakhtakor net.
The deadlock was finally broken in the 38th minute when Stanislav Andreev floated in an inviting cross from the right which picked out Zaynitdin Tadjiyev, who out-jumped Mohamed Fawzy to head past Yousuf.
Alexander Geynrikh came on at half-time for Farhod Tadjiyev, adding greater impetus to the Pakhtakor attack.
Ahmedov struck the base of the left upright a minute after the break and Geynrikh blasted a shot against the face of Khalid Mohamed as the Uzbek side turned up the pressure.
The second goal finally arrive in the 57th minute when Darko Markovic made a brilliant run through the Al Ahli defence before laying the ball off for Tadjiyev, whose shot was well save by Yousuf.
The Al Ahli keeper did brilliantly to stop the follow up by Andreev as well but could do nothing to keep out Geynrikh, who blasted the ball home at the third attempt.
The Uzbek side took their foot off the pedal in the remaining minutes but the game boiled over near the end when a fracas broke out which resulted in the dismissal of Suyunov and Al Ahli midfielder Waleed Ahmad.