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Yakubov opened the scoring after 12 minutes before Berdiev netted his second goal of the campaign from the penalty spot three minutes before half-time.
Mansur Saidov netted the third goal of Neftchi in the 62nd minute of the match, while Danilo Teixeira scored the only goal for Omani side in the fourth minute of added time.
With the win following up a 2-2 draw in India with Salgaocar two weeks ago after Neftchi began their campaign with a 2-1 home win over Jordan's Al Wehdat, Yuriy Sarkisyan's side are certain to maintain top spot in Group D at the halfway mark ahead of next week's trip to Oman.