The third-seeded Stephens, who had a first-round bye, lost her opening service games in each set.
Stephens, the 2017 US Open champion, secured qualification for the WTA Finals last week after a strong season which included reaching the French Open final.
The fifth-ranked Pliskova lost to Russian veteran Vera Zvonareva 6-1, 6-2, giving the idle Svitolina a spot in the tournament in Singapore.
Kiki Bertens then lost to Aliaksandra Sasnovich 6-3, 4-6, 6-3 a short time later, handing Pliskova the final spot. Bertens, however, could still make it if top-ranked Simona Halep skips the tournament with a back injury. Halep withdrew from the Kremlin Cup because of the injury.