There is weekly train from Mangalore to Puducherry which leaves from Podanur at 12:15 a.m and reaches Poducherry at 8 a.m. Information from 90di.com:
Train:

Puducherry Exp (6044)
Departs:
12:15...
more...

AM
from Podanur Jn (PTJ)
Arrives:
8:00 AM
at Puducherry (PDY)
Rs. 178
Duration: 7hour 45minute
Operates on Tue
But in the return direction the train reaches Podanur at 12.05 a.m. Podanur junction does not sufficient public transport facilities between 10.00 p.m to 6.00 a.m. The second track between Irugur and Cbe has already been put into use, though unofficially. It would be better the frequency of this train is increased and routed through cbe then it will be of immense use providing the much needed east-west link train of Tamilnadu.