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Luiz Felipe Scolari's side, whose AFC Champions League campaign was ended by Al Hilal in midweek, went ahead in the 57th minute through Anzur Ismailov before Timur Kapadze added a second with 13 minutes remaining.
Dilshod Sharofetdinov converted a late penalty for Navbakhor but it was not enough to deny Bunyodkor a sixth win from eight games.
Elsewhere, Nasaf - the only other team unbeaten in the league so far this season - were held to a goalless draw by Olmaliq.
In other games, Samarqand defeated Neftchi 3-1, Mash'al edged Locomotiv 1-0, Shurtan defeated Khorezm 2-0 and Qyzylqum edged Andijan 2-1.