After dropping a tough first set, 4-6, the second-seeded Nadal bounced back to improve to 5-0 against Baghdatis this season.
"I said before the tournament I just want to play good because my goal is finish the season with good feelings," Nadal said.
In Sunday’s final, the Spaniard faces Argentina's David Nalbandian, a 6-2, 6-4 winner over 10th-seeded Frenchman Richard Gasquet in the day's second semifinal.
Despite his loss, Gasquet has qualified for the season-ending eight-man Tennis Masters Cup at Shanghai starting next Saturday.
Sunday's Nadal-Nalbandian winner will earn a first prize check of $491,412, with the runner-up claiming $245,706.