#STEP #1

Set innodb_file_per_table to 0 in /etc/my.cnf

    [mysqld]
    innodb_file_per_table = 0

#STEP #2

    service mysql restart

#STEP #3

Convert every InnoDB table to InnoDB again

    echo "SET SQL_LOG_BIN = 0;" > /root/ConvertInnoDBToInnoDB.sql
    MYSQL_CONN="-u... -p..."
    SQL="SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=InnoDB;')"
    SQL="${SQL} FROM information_schema.tables WHERE engine='InnoDB'"
    mysql ${MYSQL_CONN} -AN -e"" >> /root/ConvertInnoDBToInnoDB.sql
    less /root/ConvertInnoDBToInnoDB.sql

Once you view he script and are satisfied, login to mysql and run this

    mysql> source /root/ConvertInnoDBToInnoDB.sql

#EPILOGUE

All `.ibd` files will vanish and all InnoDB tables and indexes will exist inside ibdata1

#Give it a Try !!!