Muguruza used a solid forehand to power through the first set during which she hit just eight unforced errors but gave up 20 in the second as Williams forced a decider.
The Spaniard fell behind in the third set before responding immediately with a break. She clinched the match when seven-times grand slam champion Williams sent a forehand wide.
With the win, world number seven Muguruza will return to the top five in the rankings and be guaranteed a top-four seeding at Roland Garros for the year's second grand slam.
In other action, Romanian sixth seed Simona Halep swept into the semi-finals of the Italian Open in Rome by beating Estonian qualifier Anett Kontaveit 6-2 6-4 on Friday.
She will now play Dutch 15th seed Kiki Bertens, who saw off Australian qualifier Daria Gavrilova 6-3 6-3, in Saturday's semi-final on the red Foro Italico clay.
"Today was a good match, but I can say that I could finish earlier in the second set," said Halep, who raced to a 3-0 lead in the first set and broke Kontaveit in the opening game of the second before winning.
"But she turned it a little bit around ... she came back for a few games, and she played really, really well."
(Reporting by Alan Baldwin in London; Additional reporting by Frank Pingue in Toronto; Editing by Pritha Sarkar)
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