Malappuram resident Kanakadurga, 46, and Kozhikode local Bindu said that they began climbing the steps to Lord Ayyappa shrine around midnight and reached the temple at 3:45 am for darshan. Mr Vijayan's government supports the court verdict allowing women to enter the temple.
Organisers say as many as 3 million women joined what they are calling the "women's wall".
Last year, violent protests broke out in the state after India's top court in September ordered the authorities to lift the ban on women or girls of menstruating age from entering the temple, which draws millions of worshippers a year.
On Tuesday, the state government backed a protest by thousands of women, who formed a 620 km (385 mile) human chain, termed the "women's wall", in support of "gender equality" and access to the temple.
"Those who have tried to purify the temple today after the women entered are standing against the constitution of this country".
The women's claims have not been verified yet.
The Supreme Court decision to let women worship at the Sabarimala shrine came after a petition argued that the custom banning them violated gender equality. Protesters blocked several roads and threw stones at law enforcement officials, sparking clashes, said Kumar, adding that police fired tear gas to quell the violence.
Protesters in Kerala's capital city of Thiruvananthapuram block traffic and shout slogans reacting to reports of two women of menstruating age entering the Sabarimala temple, one of the world's largest Hindu pilgrimage sites, on Wednesday.
Kerala Chief Minister Pinarayi Vijayan has confirmed that women have entered the Sabarimala shrine.
Two women devotees, below the age of 50 years, entered the Sabarimala temple on early Wednesday morning.
The minister had made the appeal after the protestors forced a six-member group from Tamil Nadu and two women from north Kerala to abandon their attempt to enter the temple during the peak Mandalakala pilgrim season.
"This is a massive victory for the women of India. It is to be done openly, everybody should accept, that's our view", CPI general secretary Suravaram Sudhakar Reddy said.
Women are still barred from a handful of Hindu temples in India. 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.
Policemen outside the Sabarimala temple. The temple is dedicated to the god Ayyappan, believed to be the son of Shiva and Vishnu.
The Supreme Court is to hear challenges to its landmark ruling from January 22.