The seven-times grand slam singles champion was ranked 139th in the world at the entry deadline for the U.S. Open, while the cut-off for automatic main draw entries was 102.
The 24-year-old Williams, now up to 79th, won the tournament in 1999 and 2002.
Joining Williams as wildcard entries into the singles draw are former top 10 players Chanda Rubin and Australian Alicia Molik.
The two-week U.S. Open begins on Aug. 28.