Problém je v tom, že CLASSPATH by měly být odděleny dvojtečkou, zatímco JARS by měly být odděleny čárkami:
$SPARK_HOME/bin/spark-submit \
--driver-class-path /usr/local/share/mongo-hadoop/build/libs/mongo-hadoop-1.5.0-SNAPSHOT.jar:/usr/local/share/mongo-hadoop/spark/build/libs/mongo-hadoop-spark-1.5.0-SNAPSHOT.jar \
--jars /usr/local/share/mongo-hadoop/build/libs/mongo-hadoop-1.5.0-SNAPSHOT.jar,/usr/local/share/mongo-hadoop/spark/build/libs/mongo-hadoop-spark-1.5.0-SNAPSHOT.jar my_application.py