diff --git a/core/includes/schema.inc b/core/includes/schema.inc
index e4e2a29..bf2b300 100644
--- a/core/includes/schema.inc
+++ b/core/includes/schema.inc
@@ -106,7 +106,10 @@ function drupal_set_installed_schema_version($module, $version) {
   \Drupal::keyValue('system.schema')->set($module, $version);
   // Store the information in config so that we can ensure that database updates
   // are the same between the source and the target site instances.
-  \Drupal::configFactory()->getEditable('core.extension')->set("versions.$module.schema", (string) $version);
+  \Drupal::configFactory()
+    ->getEditable('core.extension')
+    ->set("versions.$module.schema", (string) $version)
+    ->save();
   // Reset the static cache of module schema versions.
   drupal_get_installed_schema_version(NULL, TRUE);
 }
diff --git a/core/modules/config/src/Tests/ConfigImporterTest.php b/core/modules/config/src/Tests/ConfigImporterTest.php
index a07bcce..4dc2367 100644
--- a/core/modules/config/src/Tests/ConfigImporterTest.php
+++ b/core/modules/config/src/Tests/ConfigImporterTest.php
@@ -697,7 +697,7 @@ public function testVersionMismatch() {
       $error_log = $this->configImporter->getErrors();
       $this->assertEqual([
         'The schema version of <em class="placeholder">config_test</em> module on the source site (8999) does not match this site (-1).',
-        'The version of <em class="placeholder">system</em> module on the source site (8.0.0-beta1) does not match this site (8.0.0-dev).'
+        'The version of <em class="placeholder">system</em> module on the source site (8.0.0-beta1) does not match this site (' . \Drupal::VERSION . ').'
       ], $error_log);
     }
   }
diff --git a/core/modules/system/src/Tests/Update/VersionInfoUpdateTest.php b/core/modules/system/src/Tests/Update/VersionInfoUpdateTest.php
new file mode 100644
index 0000000..280cbe8
--- /dev/null
+++ b/core/modules/system/src/Tests/Update/VersionInfoUpdateTest.php
@@ -0,0 +1,64 @@
+<?php
+
+/**
+ * @file
+ * Contains \Drupal\system\Tests\Update\VersionInfoUpdateTest.
+ */
+
+namespace Drupal\system\Tests\Update;
+
+/**
+ * Tests the upgrade path for adding version information to core.extension.
+ *
+ * @see system_update_8015()
+ *
+ * @group Update
+ */
+class VersionInfoUpdateTest extends UpdatePathTestBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  protected function setDatabaseDumpFiles() {
+    $this->databaseDumpFiles = [
+      __DIR__ . '/../../../../system/tests/fixtures/update/drupal-8.bare.standard.php.gz',
+    ];
+  }
+
+  /**
+   * Tests that core.extension:versions is updated properly.
+   */
+  public function testSystemUpdate8015() {
+    // Set a partial value to ensure that regardless everything is updated
+    // correctly.
+    $this->config('core.extension')->set('versions.user.install', '8.0.0')->save();
+    $this->runUpdates();
+
+    // Test that a module is added.
+    $this->assertEqual([
+      'current' => \Drupal::VERSION,
+      'install' => \Drupal::VERSION,
+      'schema' => drupal_get_installed_schema_version('system'),
+    ], $this->config('core.extension')->get('versions.system'));
+    // Test that a profile is added.
+    $this->assertEqual([
+      'current' => \Drupal::VERSION,
+      'install' => \Drupal::VERSION,
+      'schema' => drupal_get_installed_schema_version('standard'),
+    ], $this->config('core.extension')->get('versions.standard'));
+    // Test that a theme is added.
+    $this->assertEqual([
+      'current' => \Drupal::VERSION,
+      'install' => \Drupal::VERSION,
+    ], $this->config('core.extension')->get('versions.bartik'));
+
+    // Test that any existing version information is merged correctly.
+    $this->assertEqual([
+      'current' => \Drupal::VERSION,
+      'install' => '8.0.0',
+      'schema' => drupal_get_installed_schema_version('user'),
+    ], $this->config('core.extension')->get('versions.user'));
+
+  }
+
+}
diff --git a/core/modules/system/system.install b/core/modules/system/system.install
index 67d049a..076e065 100644
--- a/core/modules/system/system.install
+++ b/core/modules/system/system.install
@@ -10,6 +10,7 @@
 use Drupal\Core\Url;
 use Drupal\Core\Database\Database;
 use Drupal\Core\DrupalKernel;
+use Drupal\Core\Extension\Extension;
 use Drupal\Core\Site\Settings;
 use Drupal\Core\StreamWrapper\PrivateStream;
 use Drupal\Core\StreamWrapper\PublicStream;
@@ -1873,27 +1874,49 @@ function system_update_8014() {
  */
 
 /**
+ * @addtogroup updates-8.1.0
+ * @{
+ */
+
+/**
  * Add the version information to core.extension
  */
 function system_update_8015() {
   // Update core.extensions to have the correct version information.
   $core = \Drupal::configFactory()->getEditable('core.extension');
-  $versions = $core->get('versions');
-  foreach (\Drupal::moduleHandler()->getModuleList() as $module => $extension) {
-    $version = \Drupal::service('info_parser')->parse($extension->getPathname())['version'];
-    $versions[$module] = [
+  $versions = $core->get('versions') ?: [];
+  $info_parser = \Drupal::service('info_parser');
+
+  // Create a method to populate the version information for an array of
+  // \Drupal\Core\Extension\Extension objects.
+  $map_version_info = function (Extension $extension) use ($info_parser) {
+    // Read from disk to avoid using APIs.
+    $version = $info_parser->parse($extension->getPathname())['version'];
+    $return = [
       'current' => $version,
+      // We can't know which version was present at install time so all we can
+      // do is use the current version.
       'install' => $version,
-      'schema' => (string) drupal_get_installed_schema_version($module),
     ];
-  }
-  foreach (\Drupal::service('theme_handler')->listInfo() as $theme => $extension) {
-    $version = \Drupal::service('info_parser')->parse($extension->getPathname())['version'];
-    $versions[$theme] = [
-      'current' => $version,
-      'install' => $version,
-    ];
-  }
+    // Modules and profiles also stored the schema version.
+    if ($extension->getType() === 'module' || $extension->getType() === 'profile') {
+      $return['schema'] = (string) drupal_get_installed_schema_version($extension->getName());
+    }
+    return $return;
+  };
+
+  // It is possible that version information already exists. For example,
+  // another hook_update_N hook could have installed a module. Do not overwrite
+  // existing data.
+  $versions = \Drupal\Component\Utility\NestedArray::mergeDeep(
+    array_map($map_version_info, \Drupal::moduleHandler()->getModuleList()),
+    array_map($map_version_info, \Drupal::service('theme_handler')->listInfo()),
+    $versions
+  );
   ksort($versions);
   $core->set('versions', $versions)->save();
 }
+
+/**
+ * @} End of "addtogroup updates-8.1.0".
+ */