diff -r b9404639a18c Lib/venv/__init__.py
--- a/Lib/venv/__init__.py	Wed Jan 11 00:07:40 2017 +0100
+++ b/Lib/venv/__init__.py	Tue Jan 10 17:40:04 2017 -0800
@@ -57,13 +57,20 @@
         """
         env_dir = os.path.abspath(env_dir)
         context = self.ensure_directories(env_dir)
-        self.create_configuration(context)
+        self.create_configuration(context, force_no_site=True)
         self.setup_python(context)
         if self.with_pip:
             self._setup_pip(context)
         if not self.upgrade:
             self.setup_scripts(context)
             self.post_setup(context)
+        if self.system_site_packages:
+            # Recreate venv config file.
+            self.create_configuration(context)
+            # Remove installed site-packages files.
+            shutil.rmtree(context.libpath)
+            # Recreate empty site-packages directory.
+            os.mkdir(context.libpath)
 
     def clear_directory(self, path):
         for fn in os.listdir(path):
@@ -115,6 +122,7 @@
                                    'python%d.%d' % sys.version_info[:2],
                                    'site-packages')
         context.inc_path = path = os.path.join(env_dir, incpath)
+        context.libpath = libpath
         create_if_needed(path)
         create_if_needed(libpath)
         # Issue 21197: create lib64 as a symlink to lib on 64-bit non-OS X POSIX
@@ -129,7 +137,7 @@
         create_if_needed(binpath)
         return context
 
-    def create_configuration(self, context):
+    def create_configuration(self, context, force_no_site=False):
         """
         Create a configuration file indicating where the environment's Python
         was copied from, and whether the system site-packages should be made
@@ -141,7 +149,7 @@
         context.cfg_path = path = os.path.join(context.env_dir, 'pyvenv.cfg')
         with open(path, 'w', encoding='utf-8') as f:
             f.write('home = %s\n' % context.python_dir)
-            if self.system_site_packages:
+            if self.system_site_packages and not force_no_site:
                 incl = 'true'
             else:
                 incl = 'false'