| Score: | 6–3, 3–6, 7–5 |
| Draw: | 56 |
| Seeds: | 16 |
| Before Name: | Newsweek Champions Cup – Singles |
| After Name: | Indian Wells Masters – Men's singles |
| Before Name 2: | State Farm Evert Cup – Singles |
| After Name 2: | Indian Wells Masters – Women's singles |
Serena Williams defeated Steffi Graf in the final, 6–3, 3–6, 7–5 to win the women's singles tennis title at the 1999 Indian Wells Open. It was the second and last time that the two would contest a professional match.
Martina Hingis was the defending champion, but lost in the quarterfinals to Chanda Rubin.
The top eight seeds received a bye to the second round.