diff --git a/pkgs/development/python-modules/pygraphviz/default.nix b/pkgs/development/python-modules/pygraphviz/default.nix
index 8ca84e9b7c0..1fcc0ef8ce4 100644
--- a/pkgs/development/python-modules/pygraphviz/default.nix
+++ b/pkgs/development/python-modules/pygraphviz/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, buildPythonPackage, fetchPypi, graphviz
+{ stdenv, buildPythonPackage, fetchPypi, substituteAll, graphviz
 , pkgconfig, doctest-ignore-unicode, mock, nose }:
 
 buildPythonPackage rec {
@@ -10,17 +10,18 @@ buildPythonPackage rec {
     sha256 = "7c294cbc9d88946be671cc0d8602aac176d8c56695c0a7d871eadea75a958408";
   };
 
-  buildInputs = [ doctest-ignore-unicode mock nose ];
-  propagatedBuildInputs = [ graphviz pkgconfig ];
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ graphviz ];
+  checkInputs = [ doctest-ignore-unicode mock nose ];
 
   patches = [
     # pygraphviz depends on graphviz being in PATH. This patch always prepends
     # graphviz to PATH.
-    ./graphviz-path.patch
+    (substituteAll {
+      src = ./graphviz-path.patch;
+      inherit graphviz;
+    })
   ];
-  postPatch = ''
-    substituteInPlace pygraphviz/agraph.py --subst-var-by graphvizPath '${graphviz}/bin'
-  '';
 
   # The tests are currently failing because of a bug in graphviz 2.40.1.
   # Upstream does not want to skip the relevant tests:
diff --git a/pkgs/development/python-modules/pygraphviz/graphviz-path.patch b/pkgs/development/python-modules/pygraphviz/graphviz-path.patch
index dde6df967f0..e4ff925009d 100644
--- a/pkgs/development/python-modules/pygraphviz/graphviz-path.patch
+++ b/pkgs/development/python-modules/pygraphviz/graphviz-path.patch
@@ -7,7 +7,7 @@ index 8f72024..2d8358e 100644
          import glob
  
 -        paths = os.environ["PATH"]
-+        paths = '@graphvizPath@:' + os.environ["PATH"]
++        paths = '@graphviz@/bin:' + os.environ["PATH"]
          if os.name == "nt":
              exe = ".exe"
          else:
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 03341fcf61f..cc536547b21 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3141,7 +3141,7 @@ in {
   };
 
   pygraphviz = callPackage ../development/python-modules/pygraphviz {
-    graphviz = pkgs.graphviz; # not the python package
+    inherit (pkgs) graphviz pkgconfig; # not the python package
   };
 
   pymc3 = callPackage ../development/python-modules/pymc3 { };