Svitolina failed to recover from a right leg injury to start her match against world number 114 American Nicole Gibbs.
"I did everything I could possibly to get ready for today but unfortunately I hurt my elbow during practice and there was no way I could perform my best... unfortunately I have to withdraw from the tournament," Wozniacki said.
Wozniacki, who beat Eugenie Bouchard 6-1 6-1 in the opening round on Wednesday, and Svitolina have already booked their places in the season-ending WTA Finals in Singapore which take place from Oct. 22-29.
Jennifer Brady upset Chinese eighth seed Zhang Shuai 6-3 6-4 to advance to the last eight in Hong Kong. She was joined by Wang Qiang who defeated Thai Luksika Kumkhum 6-4 6-4.
(Reporting by Shrivathsa Sridhar in Bengaluru; Editing by Toby Davis)
