Williams struggled at the outset but bounced back for a 2-6, 6-3, 6-0 victory over her Chinese opponent, winning her 11th title of the year en route to more than $12 million in prize money.
Li broke twice early for a 4-1 advantage and quickly closed out the first set. She forged a 3-3 tie in the second set, but the world No. 1 then took over, reeling off wins in the next nine games.
Williams finished 2013 with a match record of 78-4, taking the season-ending title for the fourth time overall and for the second straight year.
Her 11 titles are the most for any woman since Martina Hingis won 12 in 1997.
Li, meanwhile, will jump to No. 3 in the world rankings with her Istanbul performance. She fell to 1-10 lifetime against Williams.