diff --git a/Makefile b/Makefile
index 5d662cacf4..363f031a86 100644
--- a/Makefile
+++ b/Makefile
@@ -130,7 +130,7 @@ controller-gen: ## Download controller-gen locally if necessary.
 
 KUSTOMIZE = $(shell pwd)/bin/kustomize
 kustomize: ## Download kustomize locally if necessary.
-	GOBIN=$(PROJECT_DIR)/bin go install sigs.k8s.io/kustomize/kustomize/v4@v4.5.7
+	GOBIN=$(PROJECT_DIR)/bin go install sigs.k8s.io/kustomize/kustomize/v5@v5.4.3
 
 ## Download external CRDs for the integration testings.
 EXTERNAL_CRDS_DIR ?= $(PROJECT_DIR)/manifests/external-crds
diff --git a/manifests/base/webhook/kustomization.yaml b/manifests/base/webhook/kustomization.yaml
index 1523fc1f35..bc84486cb9 100644
--- a/manifests/base/webhook/kustomization.yaml
+++ b/manifests/base/webhook/kustomization.yaml
@@ -1,15 +1,17 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
-  - manifests.yaml
-commonLabels:
-  control-plane: kubeflow-training-operator
+- manifests.yaml
 patches:
-  - path: patch.yaml
-    target:
-      group: admissionregistration.k8s.io
-      version: v1
-      kind: ValidatingWebhookConfiguration
+- path: patch.yaml
+  target:
+    group: admissionregistration.k8s.io
+    kind: ValidatingWebhookConfiguration
+    version: v1
 
 configurations:
-  - kustomizeconfig.yaml
+- kustomizeconfig.yaml
+labels:
+- includeSelectors: true
+  pairs:
+    control-plane: kubeflow-training-operator