The home side took the lead with an Ahmed Ajab header and although Pakhtakor equalised with a powerful low shot by Odil Ahmedov, the Kuwaitis restored their advantage with a Khalaf Al Salama penalty on the stroke of half-time.
Zaynitdin Tadjiyev got the Uzbeks back on level terms again with six minutes remaining but the visitors ended the match with only ten men when Ilhomjon Suyunov was sent off in stoppage time after receiving his second yellow card.
Needing a win to keep alive their hopes of reaching the knockout stage, Pakhtakor made a lively start with Ilhomjon Suyunov shooting wide and Odil Ahmedov forcing a good save out of goalkeeper Nawaf Al Khaldi.
However, it was the home side that went ahead in the 20th minute when Nawaf Al Mutairi sent in a cross from the right which was headed home by Ajab past Pakhtakor goalkeeper Ignatiy Nesterov.
The Uzbeks levelled the score in the 37th minute when the ball was laid off by Sadriddin Abdullaev for Ahmedov who smashed a powerful low shot from 25 metres into the bottom left corner of the Al Qadsia net.
Al Qadsia would regain their lead though in the second minute of stoppage time at the end of the first half when Ajab was pushed over in the box by Islom Inomov and Al Salama made no mistake, sending Nesterov the wrong way from the spot to make it 2-1.
Pakhtakor should have levelled again seven minutes into the second half when Komoliddin Tadjiyev had a powerful shot stopped Al Khaldi.
The visitors went close again in the 71st minute when Zaynitdin Tadjiyev broke clear with only the goalkeeper to beat but saw his shot saved by Al Khaldi.
Tadjiyev would finally get the ball into net in the 84th minute after running on to a hopeful long ball and leaving defender Fayez Bandar in his wake before turning his shot into the net.
As the tension mounted in the closing minutes, tempers flared and Pakhtakor were reduced to ten men when Suyunov was sent off after receiving his second yellow card in the stoppage time.