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Pakhtakor, heavily depleted after a raft of desertions, lost the second leg of the semi-final 3-2 to Neftchi but managed to qualify on an aggregate 6-4 score.
Bunyodkor had no worries, brushing aside Nasaf 2-0 for a 5-0 aggregate romp.
Akmal Holmatov and Alexander Geynrikh were on target for Pakhtakor, while it was a hat-trick from Anvar Berdiyev that gave Neftchi their confidence-boosting victory.
In the other semi-final, Anvarjon Soliev and Victor Karpenko netted the goals for Luiz Felipe Scolari’s side.
The final will be played on August 8.
Bunyodkor and Pakhtakor are involved in the AFC Champions League quarter-finals while Neftch are playing in the AFC Cup last eight.