The temple, which attracts millions of Hindu pilgrims each year, is dedicated to Lord Ayyappa, "a Hindu god who devotees believe is celibate and can not have contact with women of menstruating age", writes NPR's Lauren Frayer.
Two women made history Wednesday when they entered one of India's largest Hindu pilgrimage sites.
"If the women have entered means, they have not faced any objection".
Bindu Ammini, 42, and Kanaka Durga, 44 entered the shrine around dawn.
BBC Hindi reports that five million women from all over Kerala lined up along highways to form a chain "which stretched from the northern tip of Kasaragod to the southern end in Thiruvanthapuram".
Police were guarding the homes of the women after they left the temple and were prepared to let more women enter the temple, he said.
On Wednesday, hundreds of women in Mumbai, India's financial capital, formed a human chain to express solidarity with the women in Kerala. They have become the first women to offer prayers at Sanctum sanctorum of Lord Ayyappa shrine since the Supreme Court overturned the centuries-old tradition previous year.
The police intervened and tried to provide women with safe passage to the shrine, resulting in clashes.
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Two women were able to reach the Sabarimala temple premises in October, thanks to the protection of more than 100 police, but they were forced to retreat after a confrontation with protesters outside the temple sanctum, reported the BBC. Hours later, the chief priest or the "thantri" abruptly closed the temple doors for about an hour to conduct the purification rituals.
Later, media reported that the temple had re-opened.
The decision sparked massive protests, with crowds physically stopping women from accessing the temple.
Across cities and towns, menstruating girls and women are not allowed to prepare food, enter a temple or touch an idol. Noted activist G Mallika viewed this as a clear indication that the trouble in Sabarimala was created by right-wing activists who entered the hillock disguised as devotees.
The restriction on women at Sabarimala, situated on top of a 3,000-foot (915-metre) hill in a tiger reserve that takes hours to climb, reflects a belief - not exclusive to Hinduism - that menstruating women are impure.
An estimated one million Hindu pilgrims travel to the Sabarimala temple in the southern state of Kerala annually.