Second half goals from Ilhomjon Suyunov and Alexander Geynrikh earned the two-time semi-finalists from Uzbekistan the three points and keep their hopes of progressing to the knockout phase alive.
Following a goalless opening 45 minutes, Suyunov gave Pakhtakor the lead two minutes after the restart when Akmal Holmatov rolled a free kick into his path allowing Suyunov to score from range.
Three minutes later Pakhtakor wrapped up the points when Geynrikh scored from the penalty spot after Zaynitdin Tadjiyev was brought down.
The win moves Pakhtakor on to four points from three games after an opening day defeat at the hands of Al Qadsia and a draw with Qatari side Al Gharafa.