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Bunyodkor looked on course to appear in the final for the fifth successive Uzbekistan Cup when the second leg moved into second-half stoppage time with the 2008 AFC Champions League semi-finalists leading 1-0 on aggregate following their first-leg victory in Tashkent.
However, Turkmenistan international Artur Gevorkyan kept his nerve to convert a penalty four minutes into time added on before Nasaf went on to prevail in the shootout.
Nasaf, who travel to Thailand to take on Chonburi in the first leg of their AFC Cup quarter-final on September 13, will contest the 2011 Uzbekistan Cup final with the winner of the other semi-final between Pakhtakor and Shurtan.