The temple in Kerala state has been at the centre of a prolonged showdown between Hindu devotees supporting the ban and women activists who have been forced back several times from Sabarimala.
The women entered the hilltop temple just before dawn with police security.
"We did not enter the shrine by climbing the 18 holy steps but went through the staff gate," one of the women told local media.
Kerala state Chief Minister Pinarayi Vijayan said: "It is a fact that the women entered the shrine. Police are bound to offer protection to anyone wanting to worship at the shrine."
The women's entry into the temple is certain to provoke a new gender storm.
A spokesman for the temple's management, Sasikumar Varma, said that if priests confirmed women had entered Sabarimala "necessary purification rituals will be done."
Media reports said the head priest had ordered the temple closed for "purification".
The Supreme Court ruled on September 28 that the decades-old ban on women of menstruating age at Sabarimala, which is at the top of a hill a four-hour trek from the nearest village, was illegal.
Repeated efforts by women to enter the temple were fought back by Hindu devotees.
In October, devotees clashed with police leading to the arrest of more than 2,000 people.
On Tuesday, there was more trouble when tens of thousands of women formed a human chain across Kerala state to back the demand for women's access to the temple.
The Supreme Court is to start hearing a legal challenge to its ruling on January 22.
Many Hindu groups as well as Prime Minister Narendra Modi's nationalist Bharatiya Janata Party fiercely oppose the court ruling. They argue that the court has ignored their belief that the deity Ayyappa was celibate.