Choi birdied three of her last four holes en route to a 7-under-par 66 at Atlantis Resort's Ocean Club Golf Course, ending 54 holes at 15-under 204.
The South Korean is seeking her eighth LPGA Tour victory.
Lizette Salas fired a 66 to grab sole possession of second place at 14-under 205.
Second-round leader Jessica Korda (72) in a third-place tie with Paula Creamer (71) at 12-under. Each eagled the par-5 18th.
Third-ranked Stacy Lewis (68) gained a share of fifth at 11-under with Amelia Lewis (66) and Jenny Suh (71).
Swim Week Miami Beach 2014 [PHOTOS]