Kyrgyzstan, who needed to make up a four-goal deficit following their first-leg defeat in Tashkent, found themselves further adrift when Bunyodkor midfielder Victor Karpenko broke the deadlock at the Spartak Stadium two minutes into the second half.
The 2011 AFC Asian Cup semi-finalists held their one-goal lead until the 65th minute when Nasimov put the Uzbeks 2-0 up, just two minutes after coming off the bench to replace skipper Ulugbek Bakaev.
And Nasimov rubbed further salt into the Kyrgyz wounds when the 24-year-old forward made it 3-0 on the night and 7-0 on aggregate with his second on the stroke of full time.