El problema es que CLASSPATH deben estar separados por dos puntos, mientras que JARS debe estar separado por comas:
$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
