The fifth seed won the first set 7-5 when she converted her fifth set point, but was pegged back by Li in the second, losing it 6-2.
However, last year's Wimbledon winner regained her composure to defeat her Chinese opponent in two hours 17 minutes,
The 6-3 success in the decider made sure of victory for Kvitova, now ranked 11 in the world.
It was the 22-year-old Czech's first tournament win of the year, against someone who was also seeking to get off the mark.
Kvitova, who picked up 385,000 US dollars as a result of the success, said afterwards: "I am very glad that I won this title to start the North American hardcourt season."
Li said: "Today [Monday] wasn't my day but I am very happy with way I played this week."