A police spokesman told CNN Thursday that the women - identified only by their given names Bindu Ammini and Kankadurga - are now in an undisclosed location along with some of their relatives. He added that police fired tear gas in an effort to stop violence.
Across the state hundreds were arrested, and at least one person was killed in clashes.
The Press Trust of India news agency reported that a 55-year-old passerby who was seriously injured in rock throwing by protesters in Pandalam a town died later Wednesday.
Conservative Hindu groups say they believe women of menstruating age would defile the temple's inner shrine.
For months, the area around the Sabarimala Temple complex has been the scene of angry clashes, as protesters attempted to prevent the court's decision from being enacted.
The third to enter the temple, on Thursday night amid the throng of thousands of other devotees, was a Sri Lankan woman who reportedly lives with her family in France.
"The police took two ladies, early in the morning, they brought them into the temple. We walked two hours, entered the temple around 3.30am and did the darshan", the woman said, referring to a ritual of standing in front of the temple's Hindu image. "We are 100 percent sure that we didn't hurt people".
UGA Football Players React To Oklahoma & Notre Dame's Losses In Playoffs
The true freshman has completed 65.0 percent of his passes for 2,606 yards, 24 touchdowns and four interceptions. The Tigers (13-0) and Fighting Irish (12-0) meet in the first game of the semifinal doubleheader.
In the wake of Wednesday's visit, priests at the temple moved to "purify" the grounds, leading to the temporary closure of the site.
A senior police officer TNM spoke to said "Sasikala may have worshipped", but did not give a confirmation.
Protests broke out in several places in Kerala state after the women entered the temple.
The house of Malabar Devaswom (temple administration) board member K Sasikumar at Perambra in Kozhikode was attacked with bombs in the early hours Friday, the police said. "We fulfilled our constitutional responsibility". Progressive protesters from the Communist Party of India-Marxist, which runs Kerala's local government, were also present to support the women. We are trying to rebuild our state, a rejuvenated Kerala, a new Kerala.
In rare comments regarding the Sabarimala temple on Tuesday, Modi - running for a second term in elections later this year - appeared to support the ban, saying the matter was related to tradition.
Kerala had witnessed unprecedented violence on Thursday, a day after the two women entered the hill temple, infuriating saffron outfits, with protesters blocking roads by placing burning tyres and granite blocks.
Allow me to divert your attention from the U.S.'s controversial border wall proposal for a wall of a different sort: India's "women wall", a continuous chain of over five million women stretching almost 400 miles through the state of Kerala, India. The controversy over Sabarimala is not the first time the entry of women in religious spaces has sparked debate in India.