diff -u b/core/modules/system/system.admin.inc b/core/modules/system/system.admin.inc
--- b/core/modules/system/system.admin.inc
+++ b/core/modules/system/system.admin.inc
@@ -1740,6 +1740,7 @@
   // This form allows page compression settings to be changed, which can
   // invalidate the page cache, so it needs to be cleared on form submit.
   $form['#submit'][] = 'system_clear_page_cache_submit';
+  $form['#submit'][] = 'system_performance_settings_submit';
 
   return system_config_form($form, $form_state);
 }
diff -u b/core/modules/system/system.module b/core/modules/system/system.module
--- b/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -3042,7 +3042,8 @@
  * @see system_config_form_submit()
  * @ingroup forms
  *
- * @todo D8: Replace this temporary helper with a more sophisticated solution.
+ * @todo Replace this temporary helper with a more sophisticated solution:
+ *   http://drupal.org/node/1324618.
  */
 function system_config_form($form, &$form_state) {
   $form['actions']['#type'] = 'actions';
@@ -3050,11 +3051,20 @@
     '#type' => 'submit',
     '#value' => t('Save configuration'),
   );
-  // Add the form's primary submit handler for saving configuration values and
-  // append system_config_form_submit() to output a consistent confirmation
-  // message.
-  $form['#submit'][] = $form_state['build_info']['form_id'] . '_submit';
-  $form['#submit'][] = 'system_settings_form_submit';
+
+  // Add system_config_form_submit() to output a consistent confirmation
+  // message. Since this prevents drupal_prepare_form() from adding the form's
+  // primary submit handler, do that first, using the same logic.
+  if (!isset($form['#submit'])) {
+    $form['#submit'] = array();
+    if (function_exists($form_state['build_info']['form_id'] . '_submit')) {
+      $form['#submit'][] = $form_state['build_info']['form_id'] . '_submit';
+    }
+    elseif (isset($form_state['build_info']['base_form_id']) && function_exists($form_state['build_info']['base_form_id'] . '_submit')) {
+      $form['#submit'][] = $form_state['build_info']['base_form_id'] . '_submit';
+    }
+  }
+  $form['#submit'][] = 'system_config_form_submit';
 
   // By default, render the form using theme_system_settings_form().
   if (!isset($form['#theme'])) {
@@ -3065,6 +3075,8 @@
 
 /**
  * Form submission handler for system_config_form().
+ *
+ * @see system_config_form()
  */
 function system_config_form_submit($form, &$form_state) {
   drupal_set_message(t('The configuration options have been saved.'));