The 32-year-old American power-hitter, with a career total of 55 titles with 17 major wins, also achieved the feat in 2002 and 2009.
Williams joins Justine Henin and Martina Hingis as a three-time year-end No.1, with only Steffi Graf (8), Martina Navratilova (7), Chris Evert (5) and Lindsay Davenport (4) ahead of her.
"Serena has proven time and time again throughout her career that she is an incredible champion, both on and off the court," said WTA chairman and CEO Stacey Allaster.
"This season, she continues to rewrite the record books, proving that she is one of the sport's greatest athletes of all time."
Williams has topped the rankings six times and, on Monday, she will have held the top position for a total of 156 weeks (three years), the WTA said.
In February, she became the oldest world No.1 since computer rankings were introduced in 1975.
And this year, Williams also became the first woman to surpass $US9 million ($A9.65 million) in prize money in a single season, pushing her career earnings past $US50 million ($A53.7 million).
Williams' total of 55 career singles titles means she is tied for seventh with Davenport and Virginia Wade on the all-time list.
Navratilova holds the record for the most singles titles with an astonishing 167, including 18 grand slams. The Open era record belongs to Graf, with 22 major victories.