This is the 1993 film, The Heroic Trio.
An invisible woman is kidnapping newborn babies who are destined to be emperors and delivering them to the mysterious subterranean supernatural Evil Master. The police are powerless, and the city must be saved by three very different women who share a terrible past. Anita Mui plays the mild-mannered wife of a police inspector who's also the mask-wearing, sword-slinging and knife-throwing crime fighter, Wonder Woman. Maggie Cheung plays the shotgun-toting, hard-boiled bounty hunter, Thief Catcher. Michelle Yeoh is Invisible Woman, the troubled but determined strong right arm of the Evil Master.
The TV Tropes entry mentions more matching details such as how Evil Master puppets Invisible Woman and that the Evil Master is reduced to bones in the final fight.
Out of the Inferno: During the climax, the girls blow up the Evil Master, but things don't go that easily for them when they see his skeleton rising from the flames for a second round.
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Puppeteer Parasite: The Evil Master does this to Invisible Girl in the climax although it's a much more visible example than most. He never fully takes control of her, however, due to Heroic Willpower.
Trailer (skeletal Evil Master at 2:20)
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