Melshanthi (chief priest) Unnikrishnan Namboothiri closed the portals of the sanctum sanctorum after rendering the 'Harivarasanam', the lullaby for Lord Ayyappa, the celibate deity.
Earlier, hundreds of devotees witnessed the 'padipuja', an auspicious ritual, by standing below the sacred 18 steps, chanting Ayyappa mantras.
The doors of the shrine will now open on November 17 for the three-month-long Mandalam Makaravilakku celebrations when lakhs of devotees from the country and abroad visit the place every year.
The temple was opened Monday for the annual 'Chitira Atta Thirunal" puja to celebrate the birth anniversary of Chithira Thirunal Balarama Varma, the last king of Travancore.
It was the second time in the last three weeks that the doors of the hill temple opened after the Supreme Court had allowed entry of women of all age groups into Sabarimala.
Though the CPI(M)-led LDF government put in place high security arrangements to implement the verdict, protests by devotees, who gathered in huge numbers ignoring prohibitory orders, kept young women away from the temple complex.
Hundreds of police personnel, including armed commandos, had been deployed in the complex and nearby areas to prevent any untoward incident.
Despite high security, about 200 frenzied devotees Tuesday tried to prevent a woman pilgrim from entering the hill top shrine suspecting her to be of menstrual age and allegedly attacked a cameraman of a Malayalam television news channel.
Clapping and chanting 'Ayyappa saranam', a huge crowd of devotees shoved Lalitha Ravi (52), as police escorted her to safety.
Police at 'sannidhanam', the temple complex, said a case has been registered against 200 "identifiable" people in connection with the incident, based on her complaint.
When the situation went out of control, senior RSS leader Valsan Thillankeri, who has been camping at the shrine complex since Monday, pacified the angry agitators using a microphone and asked them to maintain calm.
Scores of devotees shouted at Vishnu, the cameraman of a Malayalam TV news channel, as he was taking visuals of their protests.
A group of young women from Andhra Pradesh had to return from the base camp, Pamba, following protests this morning.
Another batch of women from the state, aged above 50, were prevented by devotees at 'nadappandal', the area near sacred 18 steps, as they did not carry the 'irumudikettu' (holy bundle containing offerings).
But police later escorted the aged women to the shrine complex after convincing devotees.
Girls below 10 years and women above 50 have frequently prayed at the Lord Ayyappa temple in the past.
However, the entry of women of all ages has become a sensitive issue after the September 28 apex court verdict.
Several journalists had been attacked by devotees when the temple was opened for six days on October 17 for the first time after the SC order.
Attempts by around a dozen women, including activists and journalists in the 10-50 age group, to script history came to nought as protests by devotees forced them to retreat.