The two women from Kerala, Bindu and Kanakadurga, who are in their 40s, entered the temple premises and offered prayers at around 3:45 am on Wednesday, reports said. The ban was informal for many years, but became law in 1972.
The temple administration closed the shrine's doors after the chief minister's confirmation of the women's entry to purify the shrine dedicated to celibate Lord Ayyappa.
The two women entered the temple, which is a four-hour uphill trek from the nearest village, under police protection just before dawn.
The women said they began from Pamba, Sabarimala's base camp, at 1.30 am today.
The workers hurled stones at the women and policemen, injuring three personnel, police said, adding that they had to fire in the air and burst teargas shells to disperse the attackers. "It is a golden moment for women to show that it is they have got a right to enter the temple and no one can stop them from doing so".
"If the women have entered means, they have not faced any objection". There were no immediate reports of injuries.
On Tuesday, a 620-km human wall was formed by women in Kerala "in support of gender equality" from Kasargod in the north to the capital, Trivandrum.
Millions of Indian women have joined hands along the roads and highways of Kerala state on the first day of the year 2019 to send a strong message of gender equality. This ban was struck down by the Supreme Court in September.
Extending support to the campaign, women from several organisations and social activists came together to form a almost one km-long human chain from Dadar Chowpatty to Shivaji Park in Mumbai on Tuesday evening. "Some believe that's because such women are impure".
Women's rights activist Trupti Desai, the leader of Bhumata Brigade who led the campaign for women to be allowed to offer prayers in Maharashtra's Shani Shingnapur temple, Haji Ali Dargah, Mahalakshmi temple and Trimbakeshwar Shiva temple, hailed the courage of the two women.
"It is a fact that the women entered the shrine".
The supreme court is to hear challenges to its landmark ruling from 22 January.
But India's ruling Hindu nationalist Bharatiya Janata Party (BJP) has argued that the court ruling is an attack on Hindu values. The court ordered the temple to immediately admit women of all ages, but since then, "hundreds of thousands of protesters, male and female devotees and some right-wing Hindu politicians have turned out to block women from approaching the temple", NPR previously reported.
In October, devotees clashed with police in a town near the temple leading to the arrest of more than 2,000 people.