Najeeb (55) was rescued from his crushed car after an hour-long operation.
Another youth, Jibin Joy (23), sustained grievous injuries in the accident and was admitted to a private hospital in Angamaly.
They were pulled out on wheeled stretchers through a 90-centimetre (3 feet) wide steel pipe, with the entire process being completed in about an hour.
Two other pilgrims in the car who suffered injuries have been shifted from Peerumedu Taluk Hospital to Kottayam MCH.
The bike he was riding collided with a bus while attempting to overtake a car at Anakkayam checkpost near Manjeri.
Bad weather was approaching with thunderstorms, hail and lower temperatures expected in the mountains but rescue organisers said they would handle it.
The possibility of outsiders entering the auditorium during programmes held at night cannot be ruled out.
Meanwhile, the National Disaster Management Authority on Sunday said that work is on to retrieve broken parts of the auger machine and start manual digging.
The incident occurred during a music concert inside a college auditorium.
The drivers and conductors of the buses suffered serious injuries in the accident.