Williams lost in the first round of the French Open on May 26. The 33-year-old Williams also missed Wimbledon, after 16 consecutive appearances, because of a lower back injury.
"I wasn't really expecting to play that well in the first set," Williams said. "So I think that in the second, I just kind of didn't handle it well. But I was pretty close there to closing that match out and then got down in the third."
In other matches, American qualifier Lauren Davis edged Svetlana Kuznetsova 3-6, 7-5, 7-5; Dominika Cibulkova stopped Angelique Kerber 6-7 (0), 6-2, 7-5; Canada's Eugenie Bouchard beat Alisa Kleybanova 6-3, 6-1.
Cibulkova needed nearly 3 hours to win the match.
"My serve was not working like I was expecting," she said. "But in the end I made it, so I was really happy."
Bouchard, a 19-year-old from Montreal, mixed up her effective ground strokes with some slick cut shots that left her Russian opponent stymied. There were more service breaks than holds early in the 79-minute match, which forced the Canadian to adjust her style.
"I just decided to go for it and started to play aggressive," Bouchard said. "That definitely helped me."
Earlier in the week, Bouchard teamed with Monica Seles for an exhibition against the Williams sisters and dropped her first-round doubles match with Flipkens.
Bouchard battled some early nerves against Kleybanova but quickly settled in. The 62nd-ranked wild-card entry looked smooth and quite comfortable for someone in her first full season on the pro circuit.
"Yeah, I am relaxed," she said. "It's fun. It's just fun being home where people know you a bit more. But besides that I know I need to stay focused on what I need to do or else I will lose my concentration.
"So I put pressure on myself and that's really all I think about -- my own expectations."
In other matches, Magdalena Rybarikova of Slovakia defeated Alexandra Dulgheru of Romania 6-4, 6-3; Italy's Francesca Schiavone defeated South Africa's Chanelle Scheepers 2-6, 6-3, 6-3; third-seeded Agnieszka Radwanska of Poland beat Belgium's Yanina Wickmayer 6-2, 6-3 while Sam Stosur, the No. 12 seed from Australia, defeated Julia Glushko of Israel 5-7, 6-2, 6-3.