On Wednesday, Bindu Ammini, 40, and Kanaka Durga, 39, entered around dawn, BBC News reported.
A government statement issued before the event predicted five million women would participate in the protest.
"The temple has now been closed for cleaning ritual following this incident where the women forcefully entered the temple".
The Congress, which is opposing the entry of women into the temple, staged demonstrations across the state in protest against the violation of customs and rituals at the temple.
Kerala CM Pinarayi Vijayan said: "It is a fact that the women entered the shrine".
The Supreme Court on September 28 overruled a decades-old ban on women of menstruating age at Sabarimala, which is a four-hour uphill trek from the nearest village.
"This is a great way of saying how powerful women are, and how we can empower ourselves and help each other", protestor Kavita Das told BBC Hindi. "Police have given them security", Vijayan told media here. Given the early hour, it's likely there were no protesters and only a few devotees.
He also said that the closure of the temple for the purification ceremony was "100% right", adding the opposition United Democratic Front (UDF) will start an agitation across the state.
The reason for Ayyappa's refusal is because of his celibacy - one of the arguments against allowing women of menstruating age to enter.
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'Such cheap tactics are unbecoming of a state government, ' he said on Twitter. These two women have protected India's constitutional rights and smashed the walls of patriarchy.
This is the second time that both the women attempted visiting the Sabarimala hill shrine. The police have also confirmed the news. "Police are bound to offer protection to anyone wanting to worship at the shrine".
Menstruation is rarely discussed openly in India and menstrual blood is considered impure by many communities.
According to the temple's mythology, Lord Ayyappa is an avowed bachelor who has taken an oath of celibacy.
Modi's government did not immediately react to the women getting into the temple, but activists celebrated.
"Those against women's entry had openly thrown a challenge that no women in the 10-50 age group will be able to reach the "sannidhanam".
State BJP chief P.S. Sreedharan Pillai said the Kerala government will face the "wrath" of Lord Ayyappa.
Many Hindu groups and Prime Minister Narendra Modi´s nationalist Bharatiya Janata Party (BJP) oppose the ruling.