diff --git a/CHANGES b/CHANGES
index bc1072b9f..642325847 100644
--- a/CHANGES
+++ b/CHANGES
@@ -17,8 +17,8 @@ Incompatible changes
   a ``conf.py`` file sphinx-build generates.
 * The ``gettext_compact`` attribute is removed from ``document.settings``
   object.  Please use ``config.gettext_compact`` instead.
-* The order of smart_quotes is changed.  For more detail, please read a
-  description of :py:meth:`.Sphinx.add_transform()`
+* The processing order of smart_quotes and sphinx domains are changed.  For more
+  details, please read a description of :py:meth:`.Sphinx.add_transform()`
 
 Deprecated
 ----------
diff --git a/sphinx/environment/__init__.py b/sphinx/environment/__init__.py
index b69a5fd32..af76c7ab1 100644
--- a/sphinx/environment/__init__.py
+++ b/sphinx/environment/__init__.py
@@ -21,7 +21,7 @@ from os import path
 
 from docutils.frontend import OptionParser
 from docutils.utils import Reporter, get_source_line
-from six import BytesIO, itervalues, class_types, next
+from six import BytesIO, class_types, next
 from six.moves import cPickle as pickle
 
 from sphinx import addnodes, versioning
@@ -570,10 +570,6 @@ class BuildEnvironment(object):
         with sphinx_domains(self), rst.default_role(docname, self.config.default_role):
             doctree = read_doc(self.app, self, self.doc2path(docname))
 
-        # post-processing
-        for domain in itervalues(self.domains):
-            domain.process_doc(self, docname, doctree)
-
         # allow extension-specific post-processing
         if app:
             app.emit('doctree-read', doctree)
diff --git a/sphinx/io.py b/sphinx/io.py
index 826da1812..d9b28bed3 100644
--- a/sphinx/io.py
+++ b/sphinx/io.py
@@ -31,6 +31,7 @@ from sphinx.transforms.compact_bullet_list import RefOnlyBulletListTransform
 from sphinx.transforms.i18n import (
     PreserveTranslatableMessages, Locale, RemoveTranslatableInline,
 )
+from sphinx.transforms.references import SphinxDomains
 from sphinx.util import logging
 from sphinx.util.docutils import LoggingReporter
 
@@ -93,7 +94,8 @@ class SphinxStandaloneReader(SphinxBaseReader):
                   Locale, CitationReferences, DefaultSubstitutions, MoveModuleTargets,
                   HandleCodeBlocks, AutoNumbering, AutoIndexUpgrader, SortIds,
                   RemoveTranslatableInline, FilterSystemMessages, RefOnlyBulletListTransform,
-                  UnreferencedFootnotesDetector, SphinxSmartQuotes, ManpageLink
+                  UnreferencedFootnotesDetector, SphinxSmartQuotes, ManpageLink,
+                  SphinxDomains,
                   ]  # type: List[Transform]
 
     def __init__(self, app, *args, **kwargs):
diff --git a/sphinx/transforms/references.py b/sphinx/transforms/references.py
index affe4012b..1d0fefdc9 100644
--- a/sphinx/transforms/references.py
+++ b/sphinx/transforms/references.py
@@ -11,6 +11,7 @@
 
 from docutils import nodes
 from docutils.transforms.references import Substitutions
+from six import itervalues
 
 from sphinx.transforms import SphinxTransform
 
@@ -28,3 +29,13 @@ class SubstitutionDefinitionsRemover(SphinxTransform):
         # type: () -> None
         for node in self.document.traverse(nodes.substitution_definition):
             node.parent.remove(node)
+
+
+class SphinxDomains(SphinxTransform):
+    """Collect objects to Sphinx domains for cross references."""
+    default_priority = 850
+
+    def apply(self):
+        # type: () -> None
+        for domain in itervalues(self.env.domains):
+            domain.process_doc(self, self.env.docname, self.document)