diff --git a/WORKSPACE b/WORKSPACE
index 622fa4d1412..babb14b509e 100644
--- a/WORKSPACE
+++ b/WORKSPACE
@@ -18,6 +18,8 @@ load("//tensorflow:workspace.bzl", "tf_repositories")
 # Please add all new TensorFlow dependencies in workspace.bzl.
 tf_repositories()
 
+register_toolchains("@local_config_python//:py_toolchain")
+
 load("@io_bazel_rules_closure//closure:defs.bzl", "closure_repositories")
 
 closure_repositories()
diff --git a/third_party/py/BUILD.tpl b/third_party/py/BUILD.tpl
index 1dd8ab433a3..3a0be1b0173 100644
--- a/third_party/py/BUILD.tpl
+++ b/third_party/py/BUILD.tpl
@@ -2,6 +2,34 @@ licenses(["restricted"])
 
 package(default_visibility = ["//visibility:public"])
 
+# Point both runtimes to the same python binary to ensure we always
+# use the python binary specified by ./configure.py script.
+load("@bazel_tools//tools/python:toolchain.bzl", "py_runtime_pair")
+
+py_runtime(
+    name = "py2_runtime",
+    interpreter_path = "%{PYTHON_BIN_PATH}",
+    python_version = "PY2",
+)
+
+py_runtime(
+    name = "py3_runtime",
+    interpreter_path = "%{PYTHON_BIN_PATH}",
+    python_version = "PY3",
+)
+
+py_runtime_pair(
+    name = "py_runtime_pair",
+    py2_runtime = ":py2_runtime",
+    py3_runtime = ":py3_runtime",
+)
+
+toolchain(
+    name = "py_toolchain",
+    toolchain = ":py_runtime_pair",
+    toolchain_type = "@bazel_tools//tools/python:toolchain_type",
+)
+
 # To build Python C/C++ extension on Windows, we need to link to python import library pythonXY.lib
 # See https://docs.python.org/3/extending/windows.html
 cc_import(
diff --git a/third_party/py/python_configure.bzl b/third_party/py/python_configure.bzl
index d1b1e594921..e07aaf687a2 100644
--- a/third_party/py/python_configure.bzl
+++ b/third_party/py/python_configure.bzl
@@ -323,6 +323,7 @@ def _create_local_python_repository(repository_ctx):
         "numpy_include",
     )
     _tpl(repository_ctx, "BUILD", {
+        "%{PYTHON_BIN_PATH}": python_bin,
         "%{PYTHON_INCLUDE_GENRULE}": python_include_rule,
         "%{PYTHON_IMPORT_LIB_GENRULE}": python_import_lib_genrule,
         "%{NUMPY_INCLUDE_GENRULE}": numpy_include_rule,
diff --git a/third_party/toolchains/preconfig/ubuntu16.04/py/BUILD b/third_party/toolchains/preconfig/ubuntu16.04/py/BUILD
index 3cd5fdd6f21..74e6964e66e 100755
--- a/third_party/toolchains/preconfig/ubuntu16.04/py/BUILD
+++ b/third_party/toolchains/preconfig/ubuntu16.04/py/BUILD
@@ -2,6 +2,34 @@ licenses(["restricted"])
 
 package(default_visibility = ["//visibility:public"])
 
+# Point both runtimes to the same python binary to ensure we always
+# use the python binary specified by ./configure.py script.
+load("@bazel_tools//tools/python:toolchain.bzl", "py_runtime_pair")
+
+py_runtime(
+    name = "py2_runtime",
+    interpreter_path = "/usr/bin/python2",
+    python_version = "PY2",
+)
+
+py_runtime(
+    name = "py3_runtime",
+    interpreter_path = "/usr/bin/python2",
+    python_version = "PY3",
+)
+
+py_runtime_pair(
+    name = "py_runtime_pair",
+    py2_runtime = ":py2_runtime",
+    py3_runtime = ":py3_runtime",
+)
+
+toolchain(
+    name = "py_toolchain",
+    toolchain = ":py_runtime_pair",
+    toolchain_type = "@bazel_tools//tools/python:toolchain_type",
+)
+
 # To build Python C/C++ extension on Windows, we need to link to python import library pythonXY.lib
 # See https://docs.python.org/3/extending/windows.html
 cc_import(
diff --git a/third_party/toolchains/preconfig/ubuntu16.04/py3/BUILD b/third_party/toolchains/preconfig/ubuntu16.04/py3/BUILD
index a56e284d904..81bd7358254 100755
--- a/third_party/toolchains/preconfig/ubuntu16.04/py3/BUILD
+++ b/third_party/toolchains/preconfig/ubuntu16.04/py3/BUILD
@@ -2,6 +2,34 @@ licenses(["restricted"])
 
 package(default_visibility = ["//visibility:public"])
 
+# Point both runtimes to the same python binary to ensure we always
+# use the python binary specified by ./configure.py script.
+load("@bazel_tools//tools/python:toolchain.bzl", "py_runtime_pair")
+
+py_runtime(
+    name = "py2_runtime",
+    interpreter_path = "/usr/bin/python3",
+    python_version = "PY2",
+)
+
+py_runtime(
+    name = "py3_runtime",
+    interpreter_path = "/usr/bin/python3",
+    python_version = "PY3",
+)
+
+py_runtime_pair(
+    name = "py_runtime_pair",
+    py2_runtime = ":py2_runtime",
+    py3_runtime = ":py3_runtime",
+)
+
+toolchain(
+    name = "py_toolchain",
+    toolchain = ":py_runtime_pair",
+    toolchain_type = "@bazel_tools//tools/python:toolchain_type",
+)
+
 # To build Python C/C++ extension on Windows, we need to link to python import library pythonXY.lib
 # See https://docs.python.org/3/extending/windows.html
 cc_import(
diff --git a/third_party/toolchains/preconfig/win_1803/py36/BUILD b/third_party/toolchains/preconfig/win_1803/py36/BUILD
index 7b2e84bb38e..1f879b4bfe8 100644
--- a/third_party/toolchains/preconfig/win_1803/py36/BUILD
+++ b/third_party/toolchains/preconfig/win_1803/py36/BUILD
@@ -2,6 +2,34 @@ licenses(["restricted"])
 
 package(default_visibility = ["//visibility:public"])
 
+# Point both runtimes to the same python binary to ensure we always
+# use the python binary specified by ./configure.py script.
+load("@bazel_tools//tools/python:toolchain.bzl", "py_runtime_pair")
+
+py_runtime(
+    name = "py2_runtime",
+    interpreter_path = "C:/Python36/python.exe",
+    python_version = "PY2",
+)
+
+py_runtime(
+    name = "py3_runtime",
+    interpreter_path = "C:/Python36/python.exe",
+    python_version = "PY3",
+)
+
+py_runtime_pair(
+    name = "py_runtime_pair",
+    py2_runtime = ":py2_runtime",
+    py3_runtime = ":py3_runtime",
+)
+
+toolchain(
+    name = "py_toolchain",
+    toolchain = ":py_runtime_pair",
+    toolchain_type = "@bazel_tools//tools/python:toolchain_type",
+)
+
 # To build Python C/C++ extension on Windows, we need to link to python import library pythonXY.lib
 # See https://docs.python.org/3/extending/windows.html
 cc_import(
diff --git a/third_party/toolchains/preconfig/win_1803/py37/BUILD b/third_party/toolchains/preconfig/win_1803/py37/BUILD
index a120ff11e10..58ee164a7c1 100644
--- a/third_party/toolchains/preconfig/win_1803/py37/BUILD
+++ b/third_party/toolchains/preconfig/win_1803/py37/BUILD
@@ -2,6 +2,34 @@ licenses(["restricted"])
 
 package(default_visibility = ["//visibility:public"])
 
+# Point both runtimes to the same python binary to ensure we always
+# use the python binary specified by ./configure.py script.
+load("@bazel_tools//tools/python:toolchain.bzl", "py_runtime_pair")
+
+py_runtime(
+    name = "py2_runtime",
+    interpreter_path = "C:/Python37/python.exe",
+    python_version = "PY2",
+)
+
+py_runtime(
+    name = "py3_runtime",
+    interpreter_path = "C:/Python37/python.exe",
+    python_version = "PY3",
+)
+
+py_runtime_pair(
+    name = "py_runtime_pair",
+    py2_runtime = ":py2_runtime",
+    py3_runtime = ":py3_runtime",
+)
+
+toolchain(
+    name = "py_toolchain",
+    toolchain = ":py_runtime_pair",
+    toolchain_type = "@bazel_tools//tools/python:toolchain_type",
+)
+
 # To build Python C/C++ extension on Windows, we need to link to python import library pythonXY.lib
 # See https://docs.python.org/3/extending/windows.html
 cc_import(