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.
As reports of "violation of custom" at Sabarimala spread fanning out protests across the state, with the cadres of BJP, Yuva Morcha, RSS, and other organizations going on a rampage the police resorted to detaining the agitators as a preventive measure.
Kerala had witnessed massive protests by devotees opposing the entry of girls and women in the 10-50 age group into the shrine after the CPI (M)-led LDF government chose to implement the apex court verdict allowing all women to offer prayers at the temple. Police could also be seen charging at protesters who were trying to enforce a shutdown of shops in the area. The police spokesperson said demonstrators blocked several roads and threw rocks at officers.
Modi's government did not immediately react to news of the women entering the temple, but activists celebrated. The head priest shut down the temple for an hour to carry out a "purification ritual".
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The women were identified as 42-year-old Kanaka Durga and 44-year-old Bindu Ammini, who told India Today TV that the two represented "the society fighting for gender justice".
One of the women, who both remain under police guard, later told reporters: "We did not enter the shrine by climbing the 18 holy steps but went through the staff gate". "We walked two hours, entered the temple around 3.30 a.m. and did the darshan", the woman said, referring to a ritual of standing in front of the temple's Hindu image.
Kerala Chief Minister Pinarayi Vijayan, for his part, called the Women's Wall a "movement for equality, gender sensitivity, and social awakening", while The Times of India framed the event as a "historic moment for gender equality".
Hundreds of thousands of Hindus -- men, young girls and elderly women -- trek to the temple for an annual festival that usually falls around the end of the year.
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In 1991, the Kerala High Court had legalised the ban which forbade women of menstruating age from visiting the site because temple authorities believe it disrespects the celibate nature of the deity worshipped.
The Supreme Court has agreed to re-examine its decision to lift the ban, after numerous legal challenges were brought against it.
NSS, which has filed a review plea in the Supreme Court challenging its verdict, expressed hope that the top court would take a favourable decision.
The incident prompted officials from the Hindu nationalist Bharatiya Janata Party, the party of Indian Prime Minister Narendra Modi, to call for protests. Instead the state is run by a coalition of left-wing parties which have said they will enforce the court ruling.
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Protests with sporadic violence were also reported in several other towns across the state, local media said.