diff --git a/django/db/models/sql/query.py b/django/db/models/sql/query.py
index 64a3e7075b..9af7544db3 100644
--- a/django/db/models/sql/query.py
+++ b/django/db/models/sql/query.py
@@ -1204,7 +1204,8 @@ class Query(object):
 
         if negate:
             self.promote_joins(join_list)
-            if lookup_type != 'isnull' and (self.is_nullable(target) or len(join_list) > 1):
+            if (lookup_type != 'isnull' and (
+                    self.is_nullable(target) or self.alias_map[join_list[-1]].join_type == self.LOUTER)):
                 # The condition added here will be SQL like this:
                 # NOT (col IS NOT NULL), where the first NOT is added in
                 # upper layers of code. The reason for addition is that if col
@@ -1447,7 +1448,7 @@ class Query(object):
         # nothing
         if self.is_nullable(query.select[0].field):
             alias, col = query.select[0].col
-            query.where.add((Constraint(alias, col, None), 'isnull', False), AND)
+            query.where.add((Constraint(alias, col, query.select[0].field), 'isnull', False), AND)
 
         # Still make sure that the trimmed parts in the inner query and
         # trimmed prefix are in sync. So, use the trimmed_joins to make sure
diff --git a/tests/queries/models.py b/tests/queries/models.py
index 28c858557b..c8598371a6 100644
--- a/tests/queries/models.py
+++ b/tests/queries/models.py
@@ -454,3 +454,19 @@ class Program(models.Model):
 class Channel(models.Model):
     programs = models.ManyToManyField(Program)
     identifier = models.OneToOneField(Identifier)
+
+class Book(models.Model):
+    title = models.TextField()
+    chapter = models.ForeignKey('Chapter')
+
+class Chapter(models.Model):
+    title = models.TextField()
+    paragraph = models.ForeignKey('Paragraph')
+
+
+class Paragraph(models.Model):
+    text = models.TextField()
+    page = models.ManyToManyField('Page')
+
+class Page(models.Model):
+    text = models.TextField()
diff --git a/tests/queries/tests.py b/tests/queries/tests.py
index 82a8de08be..2c17cb5e76 100644
--- a/tests/queries/tests.py
+++ b/tests/queries/tests.py
@@ -24,7 +24,8 @@ from .models import (Annotation, Article, Author, Celebrity, Child, Cover,
     Node, ObjectA, ObjectB, ObjectC, CategoryItem, SimpleCategory,
     SpecialCategory, OneToOneCategory, NullableName, ProxyCategory,
     SingleObject, RelatedObject, ModelA, ModelD, Responsibility, Job,
-    JobResponsibilities, BaseA, Identifier, Program, Channel)
+    JobResponsibilities, BaseA, Identifier, Program, Channel, Page, Paragraph,
+    Chapter, Book)
 
 
 class BaseQuerysetTest(TestCase):
@@ -2638,3 +2639,25 @@ class ManyToManyExcludeTest(TestCase):
             Identifier.objects.exclude(program__channel=None).order_by('name'),
             ['<Identifier: program>']
         )
+
+    def test_ticket_12823(self):
+        pg3 = Page.objects.create(text='pg3')
+        pg2 = Page.objects.create(text='pg2')
+        pg1 = Page.objects.create(text='pg1')
+        pa1 = Paragraph.objects.create(text='pa1')
+        pa1.page = [pg1, pg2]
+        pa2 = Paragraph.objects.create(text='pa2')
+        pa2.page = [pg2, pg3]
+        pa3 = Paragraph.objects.create(text='pa3')
+        ch1 = Chapter.objects.create(title='ch1', paragraph=pa1)
+        ch2 = Chapter.objects.create(title='ch2', paragraph=pa2)
+        ch3 = Chapter.objects.create(title='ch3', paragraph=pa3)
+        b1 = Book.objects.create(title='b1', chapter=ch1)
+        b2 = Book.objects.create(title='b2', chapter=ch2)
+        b3 = Book.objects.create(title='b3', chapter=ch3)
+        q = Book.objects.exclude(chapter__paragraph__page__text='pg1')
+        self.assertNotIn('IS NOT NULL', str(q.query))
+        self.assertEqual(len(q), 2)
+        self.assertNotIn(b1, q)
+        self.assertIn(b2, q)
+        self.assertIn(b3, q)