The pop star performed the Oscar-nominated song "Be Alive" from the "King Richard" soundtrack on the tennis courts where Venus and Serena Williams began their careers.
The "Power Of The Dog" director said she "did not intend to devalue these two legendary Black women and world-class athletes" with "a thoughtless comment."
The sisters' coordinated looks were a grand slam on the red carpet.
"You can do better," the tennis legend wrote.
"King Richard," a film about the father of the tennis greats, has racked up six Oscar nominations.
"From Compton to Wimbledon to Academy awards," the 23-time Grand Slam singles champion said.
Tennis icons Venus and Serena Williams' dad, Richard, gains a hagiographical profile in the new film.
The actor received wide praise for his work in "King Richard" after the film premiered at the Telluride Film Festival in Colorado.
The actor noted the importance of celebrating "someone’s legacy while they’re still here creating it."
The movie is scheduled to hit theaters later this year.