Williams finished the 2012 season with a 59-4 record. Since her first-round loss at the French Open, the American is 31-1, winning Wimbledon, the Olympic gold medal and the U.S. Open.
But she will finish the year ranked No. 3, behind Sharapova.
Victoria Azarenka, beaten by Sharapova in the semifinals, finished the year as the top-ranked player in the world.
Williams also won the elite, year-end tournament that brings together the top eight players in the world in 2001 and 2009.