GUADALAJARA, November 18, 2013 (AFP) - Lewis had a chance to force a playoff but missed her birdie attempt.
Thompson, 18, notched her third LPGA tour title. She had claimed her second in Malaysia last month, ending the two-year dry-spell since her first triumph in 2011 when she was 16 years old.
Thompson had four birdies and one bogey in a three-under 69 at Guadalajara Country Club, and finished with a 16-under par total of 272.
Lewis was alone in second after a 68 for 273, and South Korea's Ryu So-Yeon was third after a 69 for 275.
South Korea's world number one Park In-Bee wrapped up LPGA Player of the Year honors with her fourth-placed finish, firing a 69 for 277.
Surprisingly, Park becomes the first player from South Korea to earn the award, even though the country has produced such LPGA stars as Pak Se-Ri and Shin Ji-Yai.
She is assured of the award with just the season-ending Titleholders remaining next week.
"I said all year, there should have been at least two or three girls (from South Korea) that already won the award, but nobody really did it," Park said. "It's just really hard to believe and I'm just very lucky I won."
The only player who had a slim chance to catch her for the points-based award over the final two events of the season was Norway's Suzann Pettersen, who finished tied with Thailand's Pornanong Phatlum on 278.
Thompson started the round with a one-stroke lead over South Korea's I.K. Kim, with Lewis two adrift.
But it was a head-to-head battle between Thompson and Lewis for much of the day.
Lewis fell three back with a bogey at the 11th, but recovered with birdies at 12, 13 and 14 to take a slim lead.
"Stacy is an amazing player," Thompson said. "I knew she could make a run at me any time during that round. When she made the two shot swing on me, I think on number 12, it brought it back to all squared. I knew I had to make birdies on top of her because she gets on a roll and she doesn't stop."
However, a bogey for Lewis at 17 dropped her into a tie with Thompson going into the final hole, where Thompson's five-footer dropped and Lewis's short putt to force a playoff skimmed past the edge.
"First off, I had like a 50 to 60 footer for the first one, which was interesting getting up there within a few feet," Thompson said. "On the second putt, that's what it all came down to thinking I can make it and went up to it confidently. Just knock it in."
Scores on Sunday after the final round of the LPGA Lorena Ochoa Invitational (USA unless noted, par 72):
272 - Lexi Thompson 72-64-67-69
273 - Stacy Lewis 72-66-67-68
275 - Ryu So-Yeon (KOR) 68-67-71-69
277 - Park In-Bee (KOR) 68-68-72-69
278 - Suzann Pettersen (NOR) 70-68-70-70, Pornanong Phatlum (THA) 66-69-72-71
279 - Amy Yang (KOR) 67-73-70-69, Michelle Wie 69-73-67-70, Azahara Munoz (ESP) 71-69-69-70, Lizette Salas 70-67-71-71, I.K. Kim (KOR) 70-67-67-75
280 - Chella Choi (KOR) 74-68-72-66, Anna Nordqvist SWE) 68-67-72-73
281 - Lee Il-Hee (KOR) 74-66-73-68, Jenny Shin (KOR) 69-69-75-68, Karine Icher (FRA) 70-68-72-71
282 - Mo Martin 73-69-70-70, Gerina Piller 71-65-74-72
283 - Caroline Hedwall (SWE) 73-73-69-68, Carlota Ciganda (ESP) 72-69-69-73
285 - Angela Stanford 75-72-71-67, Cristie Kerr 77-67-72-69, Ai Miyazato (JPN) 70-72-72-71, Jessica Korda 72-68-74-71
286 - Jodi Ewart Shadoff (ENG) 75-67-72-72, Brittany Lincicome 76-67-69-74
287 - Morgan Pressel 73-66-74-74
288 - Paula Creamer 74-67-77-70
289 - Catriona Matthew (SCO) 74-71-71-73
290 - Sandra Gal (GER) 72-74-74-70
293 - Alejandra Llaneza (MEX) 75-73-73-72, Meena Lee (KOR) 74-72-75-72, Margarita Ramos (MEX) 75-72-73-73, Brittany Lang 71-72-74-76
300 - Taylor Collins 74-77-76-73
WD - Beatriz Recari (ESP) 72-77