Officials said the two women, dressed in black tunics entered the Sabarimala hilltop temple in Kerala state just before dawn under police protection and left undetected.
"We did not enter the shrine by climbing the 18 holy steps but went through the staff gate," one of the women, later told reporters.
Some hours later, Indian police fired tear gas, stun grenades and water cannon as protests and clashes erupted across the southern state in reaction to the women's move.
Violent clashes were reported between scores of people in front of the state parliament in Thiruvananthapuram.
Local media says it is was the first time women have entered the temple since a landmark court ruling.
Angry clashes around the sacred site began when India's Supreme Court on September 28 declared illegal a decades-old ban on women of menstruating age at Sabarimala.
In October, Hindu traditionalists who support the ban clashed with police in a town near the temple leading to the arrest of more than 2,000 people.
On Wednesday, the temple was reportedly closed for an hour after the head priest ordered a purification ritual.
Arvind Gunarsekar, a journalist based in Delhi posted a clip of the two women outside the temple earlier on Wednesday.
Visuals of two women (Bindu and Kanaga Durga) at Sabarimala shrine earlier this morning pic.twitter.com/347z3KWAwUArvind Gunasekar (@arvindgunasekar) 2 janvier 2019
Act of defiance celebrated on social media
"Watching the visuals of them making their way into the shrine makes me cry in joy -- how long it has taken for us to claim space, to write our way into history," wrote controversial feminist author Meena Kandasamy on Twitter.
However, the move was not welcomed by everybody.
Rahul Easwar, a right-wing activist in Kerala, condemned the state authorities for helping organise the secret operation.
"Such cheap tactics are unbecoming of a state government," he said on Twitter.
On Tuesday, tens of thousands of women formed a human chain across Kerala to back the demand for women's access to the temple.
Women are still barred from a handful of Hindu temples in India.
Many Hindu groups as well as Prime Minister Narendra Modi's nationalist Bharatiya Janata Party (BJP) oppose the court ruling.
The Supreme Court is to start hearing a legal challenge to its ruling on January 22.