Repeated efforts by women to enter the temple since September have been angrily rebuffed by Hindu devotees with police having to step in to escort them away to safety.
According to TV channels, the two women, Kanakadurga, 42, and Bindu, 44, also claimed that they had entered the holy shrine of Lord Ayyappa.
Conservative Hindu groups say they believe women of menstruating age would defile the temple's inner shrine.
Meanwhile, at the pilgrim centre, the Sabarimala Tantri Kandararu Rajeevarau with the blessings of the erstwhile Pandalam royal family conducted a "purification ritual" at the shrine after the entry of Bindu and Kanakadurga. "Police have given them security", Vijayan told media here.
On Tuesday, millions of women formed a human chain more than 375 miles long from Kasargod in the northern part of the state to Thiruvananthapuram, the southernmost city and the state capital, to support gender equality.
Vijayan said in a televised news conference that the two women, who had previously tried but failed to enter the temple because their way was blocked by devotees, faced no obstruction on Wednesday. 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 a year ago.
The women, who are now under police protection, can be seen leaving the shrine in videos that have been circulating on WhatsApp.
In the midst of an ongoing battle over women's right to visit an important Hindu temple, women in the southern Indian state of Kerala lined up to form a 620km (385-mile) human chain in a mass demonstration for gender equality on Tuesday, reported the BBC.
An umbrella organisation of various pro-Hindutva groups has called for a state-wide shutdown on Thursday, amid protests at several places after entry of two women into the Lord Ayyappa temple at Sabarimala.
Two women in southern India made history early Wednesday by entering a renowned Hindu temple where women of childbearing age have not been allowed for centuries.
The ´Women´s Wall´ rally was backed by the communist government in Kerala state where the court order on Sabarimala temple has triggered weeks of protests by opponents and supporters of the ban.
Later, media reported that the temple had re-opened. Traditionally, girls and women in the menstruating age group of 10-50 years are barred at the shrine.
The decision sparked massive protests, with crowds physically stopping women from accessing the temple. 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.
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The United Arab Emirates has reopened its embassy in Syria, in a sign of improving diplomatic relations between the two countries. Trump also claimed that Saudi Arabia had agreed to finance Syria's enormous reconstruction needs.
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