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Anvarjon Soliev was the star for the Uzbek champions grabbing both goals to give the hosts the three points.
The Uzbekistan international headed home just before the half-hour from a Server Djeparov corner.
Two minutes after the break, a Rivaldo cross was headed back across goal by Edson Ramos and Soliev was on hand to nod in his second of the night.
Saleh Bashar headed one back for the Saudis with 25 minutes remaining but Bunyodkor held on for the win.
In the group’s other match, Sepahan of Iran defeated UAE’s Al Shabab 2-0.
The goals came at the beginning and at the end. Mozambique striker Armando Sá sealed the win in the last minute.