diff --git a/activerecord/lib/active_record/associations/alias_tracker.rb b/activerecord/lib/active_record/associations/alias_tracker.rb
index 92ed844a2e6c88ba765f8a0cec14c4e1c3f985e5..0248c7483ca76ebbc5ae82a36057c499f7c991a7 100644
--- a/activerecord/lib/active_record/associations/alias_tracker.rb
+++ b/activerecord/lib/active_record/associations/alias_tracker.rb
@@ -53,12 +53,18 @@ def initial_count_for(name)
           # quoted_name should be downcased as some database adapters (Oracle) return quoted name in uppercase
           quoted_name = connection.quote_table_name(name).downcase
 
-          table_joins.map { |join|
-            # Table names + table aliases
-            join.left.downcase.scan(
-              /join(?:\s+\w+)?\s+(\S+\s+)?#{quoted_name}\son/
-            ).size
-          }.sum
+          counts = table_joins.map do |join|
+            if join.is_a?(Arel::Nodes::StringJoin)
+              # Table names + table aliases
+              join.left.downcase.scan(
+                /join(?:\s+\w+)?\s+(\S+\s+)?#{quoted_name}\son/
+              ).size
+            else
+              join.left.table_name == name ? 1 : 0
+            end
+          end
+
+          counts.sum
         end
 
         def truncate(name)
diff --git a/activerecord/lib/active_record/relation/query_methods.rb b/activerecord/lib/active_record/relation/query_methods.rb
index 1654ae1eace1ef212d59b14f45d8e89236523966..7eda9ad8e8fdcfec7a7e913b086f06dd54c354ce 100644
--- a/activerecord/lib/active_record/relation/query_methods.rb
+++ b/activerecord/lib/active_record/relation/query_methods.rb
@@ -254,12 +254,12 @@ def build_joins(manager, joins)
 
       association_joins         = buckets['association_join'] || []
       stashed_association_joins = buckets['stashed_join'] || []
-      join_nodes                = buckets['join_node'] || []
+      join_nodes                = (buckets['join_node'] || []).uniq
       string_joins              = (buckets['string_join'] || []).map { |x|
         x.strip
       }.uniq
 
-      join_list = custom_join_ast(manager, string_joins)
+      join_list = join_nodes + custom_join_ast(manager, string_joins)
 
       join_dependency = ActiveRecord::Associations::JoinDependency.new(
         @klass,
@@ -267,10 +267,6 @@ def build_joins(manager, joins)
         join_list
       )
 
-      join_nodes.each do |join|
-        join_dependency.alias_tracker.aliased_name_for(join.left.name.downcase)
-      end
-
       join_dependency.graft(*stashed_association_joins)
 
       @implicit_readonly = true unless association_joins.empty? && stashed_association_joins.empty?
@@ -280,7 +276,6 @@ def build_joins(manager, joins)
         association.join_to(manager)
       end
 
-      manager.join_sources.concat join_nodes.uniq
       manager.join_sources.concat join_list
 
       manager
diff --git a/activerecord/test/cases/associations/has_many_through_associations_test.rb b/activerecord/test/cases/associations/has_many_through_associations_test.rb
index 5f2328ff95552a4ffbc612e72fdd2ea20f667274..b703c96ec1ca555d0678335f7af7c32fd8ec4342 100644
--- a/activerecord/test/cases/associations/has_many_through_associations_test.rb
+++ b/activerecord/test/cases/associations/has_many_through_associations_test.rb
@@ -821,4 +821,8 @@ def test_preloading_empty_through_association_via_joins
     assert person.posts.loaded?, 'person.posts should be loaded'
     assert_equal [], person.posts
   end
+
+  def test_explicitly_joining_join_table
+    assert_equal owners(:blackbeard).toys, owners(:blackbeard).toys.with_pet
+  end
 end
diff --git a/activerecord/test/models/toy.rb b/activerecord/test/models/toy.rb
index 79a88db0dafdf18f21935b60ba84da85cc0d51e5..6c45e99671258cd9c7052748242b648845a25e24 100644
--- a/activerecord/test/models/toy.rb
+++ b/activerecord/test/models/toy.rb
@@ -1,4 +1,6 @@
 class Toy < ActiveRecord::Base
   set_primary_key :toy_id
   belongs_to :pet
+
+  scope :with_pet, joins(:pet)
 end