The Perth side looked in firm control needing one run from three balls in their chase of 148 but Lee, who has played 76 Tests and 221 one-day internationals for Australia, was not ready to bow out without a final flourish.
Having dismissed Michael Klinger for his first wicket earlier, Lee clean bowled Nathan Coulter-Nile (seven) and Sam Whiteman (zero) with the fourth and fifth ball of the final over to give Sydney hopes of an unlikely tie.
He was right on target with his hat-trick ball but Sydney captain Moises Henriques fumbled a throw at the non-striker's end to allow Yasir Arafat, who was well short of the crease, to complete the required single for victory.
Lee finished his career with 3-25 off four overs as Perth won by four wickets to win their second consecutive title.
(Writing by Sudipto Ganguly in Mumbai; editing by Ken Ferris)
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