Solution :

This is because, the development is using old JDBC drivers, which are not compatible to Oracle 12c.

So We added the parameter SQLNET.ALLOWD_LOGON_VERSION_SERVER=8 in sqlnet.ora file under $ORACLE_HOME/rdbms/admin

For RAC system, add the parameter in sqlnet.ora file on all the nodes. And no need to restart the listener after changing sqlnet.ora.
Sometimes, parameter also need to be added in $GRID_HOME/network/admin/sqlnet.ora.

SQLNET.ALLOWED_LOGON_VERSION_SERVER=8

After adding the parameter, through JDBC connection to the database was successful.
So if you have legacy systems and facing this same, then adding this parameter will fix this issue.