The United Arab Emirates outfit came into the second leg with the upper hand having held their opponents to a 1-1 draw in the opening encounter.
And it did not take long for the hosts to go one up - Leo Lima tapping home in the sixth minute after initially seeing his penalty saved.
Ibrahima Toure then curled the ball around the visiting goalkeeper 20 minutes later to put Al Nasr firmly in control.
Jamal Rashid appeared to give Al Nahda a fighting chance of progression when he pulled one back just after the half-hour mark, but it proved to be the final goal of the match as the home side qualified for their first final in this competition.
Al Nasr will now meet fellow final debutants Saham of Oman in the decider.
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