I think the answer is CLASSPATH.
hello.py
print "Hello"
Let's run it
> python hello.py
Hello
> jython hello.py
Hello
Compile (I used py_compile to compile single file)
> jython -m py_compile hello.py
Run with java
> java -classpath d:\P\jython253\jython.jar;. hello$py
Hello
Note the dot in classpath. It is required for java to find your compiled class in current directory.