Australian pop star Kylie Minogue came second in the top 100 poll, voted for by viewers of the VH1 music channel, with Celine Dion coming in third.
Top 10 women
1. Madonna
2. Kylie Minogue
3. Celine Dion
4. Whitney Houston
5. Aretha Franklin
6. Tina Turner
7. Mariah Carey
8. Janet Jackson
9. Britney Spears
10. Kate Bush
Madonna polled 17% of the of the 750,000 votes cast, making her the clear winner.
She is the most commercially successful female artist of all time, with worldwide record sales of more than 140 million including albums True Blue, Immaculate Collection and Ray of Light.
Whitney Houston and Aretha Franklin make up the list of top five greatest females.
Despite the decline of Mariah Carey's music career following the poor reception of her last album and film, both called Glitter, she still manages to be named seventh in the list of influential artists.
Tina Turner, Janet Jackson, Britney Spears are among the eclectic mix of stars in the top 10.
The highest British entry is Kate Bush at number 10, famous for hits such as Wuthering Heights and Babooshka.
Other UK stars in the top 100 include Annie Lennox at number 14 and Dido at number 21.
The Spice Girls are placed at number 44, while members Mel C and Geri Halliwell were regarded as 58th and 62nd for their solo careers.
There was no individual entries for the other Spices, Emma Bunton, Mel B or Victoria Beckham - all of whom have been released by their record companies.
Legendary artists such as Joni Mitchell (19), Janis Joplin (28), Carol King (54), and Nina Simone (66) nestled alongside newcomers such as Pink (27), Sophie Ellis Bextor (69), Shakira (71).
The late R'n'B singer Aaliyah, who died in a plane crash in August 2001, was placed at number 24.
VH1 spokeswoman Sally Habbershaw said: "Madonna has truly reached iconic status and many of our viewers will know her entire career."