The second-ranked Russian claimed her second title of the year and 26th of her career in 42 finals appearances.
She found herself in trouble in the first set after falling to 0-4 against Na, but then turned things around, winning the next six games to force a decisive set.
Li, the reigning French Open champ, won four straight games for a 5-4 edge and went on to force a third-set tiebreak, which was delayed by two hours due to rain.
After the delay, Sharapova and Li were tied at 5-5 when Sharapova won the Rome title on her first match point.
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