Spaniard Nadal warned his fans that he was prepared to suffer ahead of his long-awaited return from injury at the exhibition event in Abu Dhabi and was rusty as Murray coasted to a straight-sets victory in Friday's semi-final.
British number one Murray's triumph came just a day after beginning the year with a more testing success over Feliciano Lopez in an encounter that lasted two and a half hours.
Nadal had been sidelined since October after cutting short last season to have his appendix removed and Murray took advantage as the world number three struggled in his first appearance of 2015.
Murray, ranked fifth, suffered a humiliating hammering at the hands of Roger Federer at the season-ending ATP World Tour Finals in London, but produced an encouraging display at the Zayed Sports City Tennis Stadium.
He broke twice to race into a 3-0 lead after saving three break points to thwart Nadal and then broke again to wrap up the first set.
Nadal gifted Murray an immediate advantage in the second set when he double-faulted and the Briton never looked back, digging deep to save a further five break points en route to victory.
"It was closer than the score suggests," Murray is quoted as saying by BBC Sport. "While he had a lot of break points I won the important ones.
"You never know how you will get on until it comes to match conditions, but it seems that all the pre-season hard work is paying off."
World number one Djokovic continued where he left off last year by easing to a 6-1 6-2 victory over Stanislas Wawrinka to reach yet another final.
The Serb reeled off nine games in a row after to seal the first set and take the upper hand in the second, with Wawrinka unable to fight back.
Nicolas Almagro beat fellow Spaniard Lopez 6-4 7-6 (8-6) in the first match to be played on Friday to ensure he will finish fifth.
