India's Supreme Court a year ago voided the ban on women aged 10-50 from entering the temple.
The judgment allowing women inside the Sabarimala Temple was the culmination of a decades-long battle to overturn the ban. They said they were accompanied by a group of police personnel in civil uniform.
Despite the Supreme Court's historic ruling on September 28 a year ago, permitting women in the 10-50 age group, no children or young women in the "barred" group were able to offer prayers at the shrine following frenzied protests by devotees and right-wing outfits.
Images show Kanaka Durga and Bindu Ammini hurrying inside with their heads bowed and wearing black tunics.
"We did not enter the shrine by climbing the 18 holy steps but went through the staff gate", one of the women, who both remained under police guard on Wednesday, later told reporters.
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 police intervened and tried to provide women with safe passage to the shrine, resulting in clashes.
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The violence started in the morning when BJP workers protesting the closure of Sabarimala temple for "purification rites" following the entry of two women early Wednesday damaged hoardings erected by the Left Democratic Front (LDF).
Two women defied a centuries-old ban on entering a Hindu temple in the Indian state of Kerala on Wednesday, sparking rowdy protests and calls for a strike by conservative Hindu groups outraged by their visit.
Chief Minister Pinarayi Vijayan has confirmed that two women had darshan at Sabarimala temple. The controversy over Sabarimala is not the first time the entry of women in religious spaces has sparked debate in India.
It is considered the spiritual home of Lord Ayyappa, a Hindu god of growth.
Reportedly, the police ensured that the women's trek was carried out in a discreet manner. The fact that the chief priest did not take the permission of the Travancore Devaswom Board (which administers the temple) or the state cabinet before conducting the rituals raised the urgency of the matter.
An estimated one million Hindu pilgrims travel to the Sabarimala temple in the southern state of Kerala annually.
The Bharatiya Janata Party's (BJP)'s Kerala state president P.S. Sreedharan Pillai called it "a conspiracy by the atheist rulers to destroy the Hindu temples", and said his party will "support the struggles against the destruction of faith by the Communists".