diff --git a/.github/workflows/sync_typeshed.yaml b/.github/workflows/sync_typeshed.yaml
index 20925a523e370..d1785034e1ca4 100644
--- a/.github/workflows/sync_typeshed.yaml
+++ b/.github/workflows/sync_typeshed.yaml
@@ -46,10 +46,6 @@ jobs:
           cp -r typeshed/stdlib ruff/crates/red_knot_vendored/vendor/typeshed/stdlib
           rm -rf ruff/crates/red_knot_vendored/vendor/typeshed/stdlib/@tests
           git -C typeshed rev-parse HEAD > ruff/crates/red_knot_vendored/vendor/typeshed/source_commit.txt
-          # Patch the typeshed stubs to include `knot_extensions`
-          ln -s ../../../knot_extensions/knot_extensions.pyi ruff/crates/red_knot_vendored/vendor/typeshed/stdlib/
-          echo "# Patch applied for red_knot:" >> ruff/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS
-          echo "knot_extensions: 3.0-" >> ruff/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS
       - name: Commit the changes
         id: commit
         if: ${{ steps.sync.outcome == 'success' }}
diff --git a/crates/red_knot_vendored/build.rs b/crates/red_knot_vendored/build.rs
index 08ad3418bff8c..965dd34025ec3 100644
--- a/crates/red_knot_vendored/build.rs
+++ b/crates/red_knot_vendored/build.rs
@@ -6,6 +6,7 @@
 //! in `crates/red_knot_vendored/vendor/typeshed` change.
 
 use std::fs::File;
+use std::io::Write;
 use std::path::Path;
 
 use path_slash::PathExt;
@@ -14,6 +15,7 @@ use zip::write::{FileOptions, ZipWriter};
 use zip::CompressionMethod;
 
 const TYPESHED_SOURCE_DIR: &str = "vendor/typeshed";
+const KNOT_EXTENSIONS_STUBS: &str = "knot_extensions/knot_extensions.pyi";
 const TYPESHED_ZIP_LOCATION: &str = "/zipped_typeshed.zip";
 
 /// Recursively zip the contents of an entire directory.
@@ -55,9 +57,14 @@ fn zip_dir(directory_path: &str, writer: File) -> ZipResult<File> {
         // Some unzip tools unzip files with directory paths correctly, some do not!
         if absolute_path.is_file() {
             println!("adding file {absolute_path:?} as {normalized_relative_path:?} ...");
-            zip.start_file(normalized_relative_path, options)?;
+            zip.start_file(&*normalized_relative_path, options)?;
             let mut f = File::open(absolute_path)?;
             std::io::copy(&mut f, &mut zip).unwrap();
+
+            // Patch the VERSIONS file to make `knot_extensions` available
+            if normalized_relative_path == "stdlib/VERSIONS" {
+                writeln!(&mut zip, "knot_extensions: 3.0-")?;
+            }
         } else if !normalized_relative_path.is_empty() {
             // Only if not root! Avoids path spec / warning
             // and mapname conversion failed error on unzip
@@ -65,11 +72,17 @@ fn zip_dir(directory_path: &str, writer: File) -> ZipResult<File> {
             zip.add_directory(normalized_relative_path, options)?;
         }
     }
+
+    // Patch typeshed and add the stubs for the `knot_extensions` module
+    println!("adding file {KNOT_EXTENSIONS_STUBS} as stdlib/knot_extensions.pyi ...");
+    zip.start_file("stdlib/knot_extensions.pyi", options)?;
+    let mut f = File::open(KNOT_EXTENSIONS_STUBS)?;
+    std::io::copy(&mut f, &mut zip).unwrap();
+
     zip.finish()
 }
 
 fn main() {
-    println!("cargo::rerun-if-changed={TYPESHED_SOURCE_DIR}");
     assert!(
         Path::new(TYPESHED_SOURCE_DIR).is_dir(),
         "Where is typeshed?"
diff --git a/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS b/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS
index 6cb47d4bfeb13..3c6898dc1a777 100644
--- a/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS
+++ b/crates/red_knot_vendored/vendor/typeshed/stdlib/VERSIONS
@@ -341,5 +341,3 @@ zipfile._path: 3.12-
 zipimport: 3.0-
 zlib: 3.0-
 zoneinfo: 3.9-
-# Patch applied for red_knot:
-knot_extensions: 3.0-
diff --git a/crates/red_knot_vendored/vendor/typeshed/stdlib/knot_extensions.pyi b/crates/red_knot_vendored/vendor/typeshed/stdlib/knot_extensions.pyi
deleted file mode 120000
index 8e6b527c81002..0000000000000
--- a/crates/red_knot_vendored/vendor/typeshed/stdlib/knot_extensions.pyi
+++ /dev/null
@@ -1 +0,0 @@
-../../../knot_extensions/knot_extensions.pyi
\ No newline at end of file