The BJP has extended support to the hartal, which is the third state-wide strike since the Supreme Court gave its verdict allowing women in the age group of 10 and 50 to enter the temple as well.
The protest comes during a fraught period for religious and gender rights in Kerala.
India's Supreme Court in September ordered the lifting of the ban on women or girls of menstruating age from entering the Sabarimala temple, which draws millions of worshippers a year. Mr Vijayan's government supports the court verdict allowing women to enter the temple.
The two women in their forties entered the temple early Wednesday and worshipped there, said Pramod Kumar, the state police spokesman.
"We reached Pampa, the main entry point to the temple at 1.30 a.m. and sought police protection to enter the temple".
Widespread protests erupted in various parts of Kerala including Kochi and Thiruvananthapuram districts after two women of menstruating age entered Sabarimala temple in the wee hours of Wednesday.
It is considered the spiritual home of Lord Ayyappa, a Hindu god of growth. The Police used water cannons and tear gas shells to disperse the protestors.
India's ruling Bharatiya Janata Party (BJP), which has pursued a Hindu nationalist agenda, has painted the September court ruling as an attack on traditional Hindu values.
Many Hindu groups and BJP oppose the ruling. They argue that the court has ignored their belief that the deity Ayyappa was celibate.
He said, " Today, two women entered #SabarimalaTemple.
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.
The temple, which attracts millions of Hindu pilgrims each year, is dedicated to Lord Ayyappa, "a Hindu god who devotees believe is celibate and can not have contact with women of menstruating age", writes NPR's Lauren Frayer. A report said the temple opened in the afternoon after completion of the ritual.
Nestled atop a steep mountain amid a lush green tiger reserve, it's the site of one of the world's largest annual pilgrimages, with millions of Hindu devotees making the journey each year.
The "women's wall" was organised by the state's left-wing coalition government.
Modi's government did not immediately react to the women getting into the temple, but activists celebrated. Police arrested more than 2,000 people in October for rioting and unlawful assembly.
The Supreme Court is to hear challenges to its landmark ruling from January 22.