diff --git a/CHANGELOG.md b/CHANGELOG.md
index 43e05b6dd0..b17f937dc6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -74,6 +74,11 @@ END_UNRELEASED_TEMPLATE
 
 {#v0-0-0-fixed}
 ### Fixed
+* (gazelle) `py_library` and `py_test` targets with missing source files are now
+  removed by Gazelle, matching the existing behavior for `py_binary` targets.
+  Previously, deleting a `.py` file in per-file generation mode left orphaned
+  targets in BUILD files, causing build failures
+  ([#3375](https://github.com/bazel-contrib/rules_python/issues/3375)).
 * (bootstrap) Fixed a potential race condition with symlink creation during
   startup.
 * (gazelle) Fixed handling of auto-included `__init__.py` files when generating `py_binary`
diff --git a/gazelle/MODULE.bazel b/gazelle/MODULE.bazel
index cff6341a2b..d2721d15ae 100644
--- a/gazelle/MODULE.bazel
+++ b/gazelle/MODULE.bazel
@@ -8,6 +8,12 @@ bazel_dep(name = "bazel_skylib", version = "1.8.2")
 bazel_dep(name = "rules_python", version = "0.18.0")
 bazel_dep(name = "rules_go", version = "0.59.0", repo_name = "io_bazel_rules_go")
 bazel_dep(name = "gazelle", version = "0.47.0", repo_name = "bazel_gazelle")
+
+git_override(
+    module_name = "gazelle",
+    commit = "73215247ebf853131af5615a3d460c43530272f1",
+    remote = "https://github.com/taowang487/bazel-gazelle.git",
+)
 bazel_dep(name = "rules_cc", version = "0.0.16")
 
 local_path_override(
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.in b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.in
new file mode 100644
index 0000000000..de50039c9b
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.in
@@ -0,0 +1,27 @@
+load(":mylib.bzl", "my_py_library", "my_py_test")
+
+# gazelle:python_generation_mode file
+# gazelle:alias_kind my_py_library py_library
+# gazelle:alias_kind my_py_test py_test
+
+my_py_library(
+    name = "bar",
+    srcs = ["bar.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+my_py_library(
+    name = "deleted_lib",
+    srcs = ["deleted.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+my_py_test(
+    name = "bar_test",
+    srcs = ["bar_test.py"],
+)
+
+my_py_test(
+    name = "deleted_test",
+    srcs = ["deleted_test.py"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.out b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.out
new file mode 100644
index 0000000000..4aa2e6cb4a
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/BUILD.out
@@ -0,0 +1,16 @@
+load(":mylib.bzl", "my_py_library", "my_py_test")
+
+# gazelle:python_generation_mode file
+# gazelle:alias_kind my_py_library py_library
+# gazelle:alias_kind my_py_test py_test
+
+my_py_library(
+    name = "bar",
+    srcs = ["bar.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+my_py_test(
+    name = "bar_test",
+    srcs = ["bar_test.py"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/WORKSPACE b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/WORKSPACE
new file mode 100644
index 0000000000..faff6af87a
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/WORKSPACE
@@ -0,0 +1 @@
+# This is a Bazel workspace for the Gazelle test data.
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/bar.py b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/bar.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/bar_test.py b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/bar_test.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/gazelle/python/testdata/remove_invalid_per_file_alias_kind/test.yaml b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/test.yaml
new file mode 100644
index 0000000000..ed97d539c0
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_alias_kind/test.yaml
@@ -0,0 +1 @@
+---
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.in b/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.in
new file mode 100644
index 0000000000..fc956023d8
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.in
@@ -0,0 +1,33 @@
+load("@rules_python//python:defs.bzl", "py_library")
+load(":mylib.bzl", "my_py_binary", "my_py_test")
+
+# gazelle:python_generation_mode file
+# gazelle:map_kind py_binary my_py_binary :mylib.bzl
+# gazelle:map_kind py_test my_py_test :mylib.bzl
+
+py_library(
+    name = "bar",
+    srcs = ["bar.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "deleted_lib",
+    srcs = ["deleted.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+my_py_binary(
+    name = "deleted_bin",
+    srcs = ["deleted_bin.py"],
+)
+
+my_py_test(
+    name = "bar_test",
+    srcs = ["bar_test.py"],
+)
+
+my_py_test(
+    name = "deleted_test",
+    srcs = ["deleted_test.py"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.out b/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.out
new file mode 100644
index 0000000000..9cd5928f6b
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_map_kind/BUILD.out
@@ -0,0 +1,17 @@
+load("@rules_python//python:defs.bzl", "py_library")
+load(":mylib.bzl", "my_py_test")
+
+# gazelle:python_generation_mode file
+# gazelle:map_kind py_binary my_py_binary :mylib.bzl
+# gazelle:map_kind py_test my_py_test :mylib.bzl
+
+py_library(
+    name = "bar",
+    srcs = ["bar.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+my_py_test(
+    name = "bar_test",
+    srcs = ["bar_test.py"],
+)
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/WORKSPACE b/gazelle/python/testdata/remove_invalid_per_file_map_kind/WORKSPACE
new file mode 100644
index 0000000000..faff6af87a
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_map_kind/WORKSPACE
@@ -0,0 +1 @@
+# This is a Bazel workspace for the Gazelle test data.
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/bar.py b/gazelle/python/testdata/remove_invalid_per_file_map_kind/bar.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/bar_test.py b/gazelle/python/testdata/remove_invalid_per_file_map_kind/bar_test.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/gazelle/python/testdata/remove_invalid_per_file_map_kind/test.yaml b/gazelle/python/testdata/remove_invalid_per_file_map_kind/test.yaml
new file mode 100644
index 0000000000..ed97d539c0
--- /dev/null
+++ b/gazelle/python/testdata/remove_invalid_per_file_map_kind/test.yaml
@@ -0,0 +1 @@
+---