The Polish third seed went down 7-5, 6-1 to the 15th seed from Ukraine.
Kostyuk, the Madrid Open winner, moved into the quarter-finals at Roland Garros for the first time in her career.
“I’m still in shock to beat such an unbelievable player who won four times here and I lost four times to her before this, I never took a set off her,” 23-year-old Kostyuk said.
Swiatek will now go another year without the title she first won in 2020 and then three times consecutively between 2022 and 2024.
With her fourth-round exit, it was the joint worst performance at Roland Garros for the 25-year-old, equal with the last-16 departure she suffered on her debut in Paris seven years ago.
The first set went on serve until the seventh game when Swiatek pounced on Kostyuk’s service to move in front.
From there, the Pole’s own delivery deserted her as the world number 15 hit back to level before the pair again exchanged another pair of breaks.
Kostyuk then dug in to hold and force the former world number one to try and serve to stay in the set.
Two Swiatek double faults gave Kostyuk the chance to claim the opener and she did with a low cross-court backhand that whizzed past her opponent at the net.
Swiatek swiftly departed the court at the interval in a bid to regroup.
She came back out firing as she immediately nosed ahead with a break to 15.
But Kostyuk was not to be denied as she sealed a three-game streak with a bruising forehand winner past a stranded Swiatek to lead 3-1.
A stunning rally concluded with a reflex volley at the net that Swiatek could not equal. In the next game a dominant Kostyuk held to love to move Swiatek to the brink.
The match was up for the six-time major winner as Kostyuk consistently pinned the Pole back with her powerful groundstrokes to win the final two games.
Kostyuk will face either seventh-seeded compatriot Elina Svitolina or Swiss 11th seed Belinda Bencic for a spot in the semi-finals.
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