The Serbian dropped the first set, 1-6, and trailed the second, 0-1, before she was overcome by the illness, and consulted a trainer before retiring to the lockeroom.
"I have a virus and I've been sick for a couple of days," Jankovic said. "I really have so much trouble breathing, and I have really been suffering on the court and I just could not play my game."
Jankovic finishes the season-ending, round-robin tennis tournament with a 1-1 record.
Jankovic had a 72-23 win-loss record this season, with titles at the ASB Classic in Auckland, New Zealand, in January; the Italian Masters at Rome in May and the Family Circle Cup at Charleston, S.C., in September.