It seems to me that in the example code that stores the uploaded file to a temporary file, you would just replace file.save(os.path.join(app.config['UPLOAD_FOLDER'], filename)) with code that uploads the file to S3 instead. 
For example, from the linked page:
def upload_file():
    if request.method == 'POST':
        file = request.files['file']
        if file and allowed_file(file.filename):
            filename = secure_filename(file.filename)
            s3 = boto.connect_s3()
            bucket = s3.create_bucket('my_bucket')
            key = bucket.new_key(filename)
            key.set_contents_from_file(file, headers=None, replace=True, cb=None, num_cb=10, policy=None, md5=None) 
            return 'successful upload'
    return ..
Or if you want to upload to S3 asynchrnously, you could use whatever queuing mechanism is provided by Heroku.