The Danish world number one recovered from the surprise loss of the second set to end a marathon baseline slugfest in two hours eight minutes at the Indian Wells Tennis Garden.
Wozniacki, beaten by Serb Jelena Jankovic in last year's final here, broke the 15th-seeded Frenchwoman three times in the final set, sealing victory when her opponent sent a backhand long.
On a cool overcast day in the California desert, the Dane threw both arms skywards to celebrate her second title of the year, having also triumphed at last month's Dubai championships.
"Marion, you had an amazing tournament this week," a jubilant Wozniacki said courtside. "I am sorry I had to beat you in the final but it's not like football where there is a draw."
Bartoli, who had booked her place in the final by crushing Belgian Yanina Wickmayer 6-1 6-3 in the last four, choked back tears as she applauded the triumphant Dane.
"Sorry I am a bit in tears but I guess it is more tears of tiredness," the 26-year-old said. "Caroline, you make me cry today. I would like to congratulate her. You can be proud of yourself.
"I know your big goal is to get a grand slam and I am sure you will get it very soon."
