Kvitova won by scores of 7-5, 2-6, 6-3 at Uniprix Stadium in a two hour, 17 minute affair, finishing off Li with an ace.
Both players were looking for their first Rogers Cup victory, and their first tour title of the season. It's a contrast from 2011, when Kvitova counted Wimbledon and the WTA Championship among her six titles.
The winner told CBC's Brenda Irving after the match that the key was being aggressive but also being patient and waiting for the right opportunities, something which eluded her in a fairly disastrous second set.
Kvitova's win was her first title in North America, earning her a payday of $360,000 US.
"It's great to have a good result in North America before the U.S. Open and I'm very glad that finally I played well [here]," said Kvitova, who went just 3-4 in previous years at the Rogers Cup.
In addition to entertaining, it was a fascinating, and at times, strange match played in front of a crowd that included Olympic diver Alexandre Despatie, Liberal MP Justin Trudeau and his wife Sophie Gregoire, and film director Denys Arcand..
The first set was filled with compelling points and breaks of serve, the second stanza illustrated why Kvitova is known as a talented but streaky player, and the final frame demonstrated why some believe she can be the next great signature women's player.
Li took home $180,000, but the 2011 French Open winner has now gone 0-3 in tournament finals this year.
"She's very tough," said Li, now 2-2 lifetime against Kvitova. "She plays the ball so deep. I felt I was always on defence. The last two matches I felt I could be aggressive on the court, but this one I felt I was 70 per cent of the time on defence."
The breaks started with the third game in the first set, with Li going up 2-1.
The fifth seed Kvitova broke in the ninth game of the first set to go up 5-4 but missed an open court shot to help Li break back. Li fell behind love-30 on her serve but tied the set.
Kvitova did her one better, losing the first three points on her serve before storming back with powerful groundstrokes to take the game and a 6-5 lead.
Li fought off four set points in the next games before eventually capitulating, with the set lasting just over an hour.
Kvitova squandered the momentum, racking up the unforced errors early in the second. She failed to register a single point through four games of the middle set.
The two top players saved their best tennis for the final set, remaining on serve until Kvitova broke through for a 4-2 lead.
Kvitova hopes to reverse the pattern from her 2011 summer. After Wimbledon, she struggled badly and lost in the first round of the U.S. Open.
"I hope this is good preparation," she said. "I played some good matches here and I hope that will continue, but every tournament is different and every player is tough, so we'll see.
Both players are scheduled to compete in Cincinnati, which began play on Monday.
Under agreement with the WTA, organizers had a private jet waiting at the airport to take the finalists to the next tour stop.