You might have to check the value of =org-babel-python-wrapper-method=, which defines the format of the created temporary file to which the source block is exported so it can be executed properly.

After installing matplotlib using pip3 and changing =org-babel-python-command= to python3 I was able to execute this example without a problem.

The value of =org-babel-python-wrapper-method= for me is:

  def main():
  %s

  open('%s', 'w').write( str(main()) )"