Henin cruised past Jelena Jankovic 6-2, 6-2 at the season-ending tournament.
Williams was treated by the tournament doctor before the start of the ninth game. She retired after losing the first set 6-4 to seventh-ranked Anna Chakvetadze.
WTA officials said Williams was expected to get a scan of her knee. In 2003, Williams had knee surgery and missed 10 events in 2006 because of knee problems.
The fifth-ranked Williams has reached the final in all three previous appearances at the event, which features the top eight players.
If Williams is not fit to face Henin on Thursday, Wimbledon finalist Marion Bartoli will replace her for the last two matches of the round-robin tournament.
Henin broke serve six times to win her 22nd straight match and improve to 9-0 against the third-ranked Serbian. Jankovic qualified for the tournament for the first time.
Although Jankovic had opportunities in the second set, Henin broke serve in the first and third games.
"From the first point to the end, I took all of my chances, all of the opportunities," Henin said. "It was her first match, so maybe I had a little advantage because I could play last night."
Later Wednesday, Ana Ivanovic plays Daniela Hantuchova.
[Associated Press; By MIKE FITZPATRICK]
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