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."
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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."
STORMING START
The final began on a surprisingly cool, overcast morning at the California desert venue and Wozniacki, despite failing to hold serve in the third game of the match, broke her opponent three times to storm through the first set in 27 minutes.
The Dane continually moved the Frenchwoman from side to side with punishing ground strokes in lengthy rallies and seemed to be heading for a straight sets demolition.
Bartoli then raised her performance several notches in the second set, breaking Wozniacki in the second and seventh games, after the Dane pushed a backhand wide, to level the match.
The ebb and flow spilt into the final set as Wozniacki regained control with her baseline dominance.
She broke Bartoli's serve in the first game and again in the fifth, when the Frenchwoman double-faulted, to take a commanding 4-1 lead before she was herself broken in the sixth.
However the Dane regained her poise to break Bartoli's serve for a final time in the ninth game, sealing victory on her second match point after her opponent struck a double-handed backhand long.
(Editing by Frank Pingue; To query or comment on this story email sportsfeedback@thomsonreuters.com)
