diff --git a/MODULE.bazel b/MODULE.bazel
index bed1787fc6..f9f173d8f1 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -84,17 +84,7 @@ bazel_dep(name = "bazel_ci_rules", version = "1.0.0", dev_dependency = True)
 # We use `WORKSPACE.bzlmod` because it is impossible to have dev-only local overrides.
 bazel_dep(name = "rules_go", version = "0.41.0", dev_dependency = True, repo_name = "io_bazel_rules_go")
 bazel_dep(name = "rules_python_gazelle_plugin", version = "0", dev_dependency = True)
-bazel_dep(name = "gazelle", version = "0.33.0", dev_dependency = True, repo_name = "bazel_gazelle")
-single_version_override(
-    module_name = "gazelle",
-    patch_strip = 1,
-    patches = [
-        # Can be removed once https://github.com/bazel-contrib/bazel-gazelle/issues/1959
-        # is fixed and released.
-        "patches/gazelle_native_sh.patch",
-    ],
-    version = "0.33.0",
-)
+bazel_dep(name = "gazelle", version = "0.40.0", dev_dependency = True, repo_name = "bazel_gazelle")
 
 internal_dev_deps = use_extension(
     "//python/private:internal_dev_deps.bzl",
diff --git a/patches/gazelle_native_sh.patch b/patches/gazelle_native_sh.patch
deleted file mode 100644
index 836fe7ca8c..0000000000
--- a/patches/gazelle_native_sh.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-
-diff -u -r a/def.bzl b/def.bzl
---- a/def.bzl	2024-11-08 13:42:27.733022366 -0800
-+++ b/def.bzl	2024-11-08 13:44:45.089900166 -0800
-@@ -16,6 +16,7 @@
-     "@bazel_skylib//lib:shell.bzl",
-     "shell",
- )
-+load("@rules_shell//shell:sh_binary.bzl", "sh_binary")
- load(
-     "@bazel_gazelle_is_bazel_module//:defs.bzl",
-     "GAZELLE_IS_BAZEL_MODULE",
-@@ -185,7 +186,7 @@
-         tags = tags,
-         **kwargs
-     )
--    native.sh_binary(
-+    sh_binary(
-         name = name,
-         srcs = [runner_name],
-         tags = tags,
-diff -u -r a/MODULE.bazel b/MODULE.bazel
---- a/MODULE.bazel	2024-11-08 13:42:23.860997684 -0800
-+++ b/MODULE.bazel	2024-11-08 13:43:46.961528172 -0800
-@@ -8,6 +8,7 @@
- bazel_dep(name = "protobuf", version = "3.19.6", repo_name = "com_google_protobuf")
- bazel_dep(name = "rules_go", version = "0.41.0", repo_name = "io_bazel_rules_go")
- bazel_dep(name = "rules_proto", version = "4.0.0")
-+bazel_dep(name = "rules_shell", version = "0.2.0")
-
- go_sdk = use_extension("@io_bazel_rules_go//go:extensions.bzl", "go_sdk")
-