Federer, who led Hewitt 18-8 in meetings between the former world number ones going into the contest, committed 22 unforced errors on his way to being broken three times in the first set after reaching the final without dropping serve once.
The world number six improved markedly in the second set but a failure to convert seven break opportunities in the third proved costly, as the Australian held on for victory in two hours and seven minutes.
The victory secured Hewitt's first ATP title since Halle in 2010 when he also beat Federer in the final, ending a 15-match losing run against his opponent.
The match was Federer's last competitive outing before the Australian Open begins on January 13, where the Swiss will be seeking to add to his record 17 grand slam titles with a fifth Melbourne crown.
(Editing by John O'Brien)
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