diff --git a/.github/workflows/run-system-tests.yaml b/.github/workflows/run-system-tests.yaml
index 9b97ea5c167..c6f35bd91cc 100644
--- a/.github/workflows/run-system-tests.yaml
+++ b/.github/workflows/run-system-tests.yaml
@@ -72,7 +72,7 @@ jobs:
     with:
       library: java
        # If you change the following comment, update the pattern in the update_system_test_reference.sh script to match.
-      ref: main # system tests are pinned on release branches only
+      ref: "main" # system tests are pinned on release branches only
       binaries_artifact: binaries
       desired_execution_time: 900  # 15 minutes
       scenarios_groups: tracer-release
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a1c4a61c2f3..6efc0ef2467 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1071,7 +1071,7 @@ publishing-gate:
 
 configure_system_tests:
   variables:
-    SYSTEM_TESTS_REF: main # system tests are pinned on release branches only
+    SYSTEM_TESTS_REF: "main" # system tests are pinned on release branches only
     SYSTEM_TESTS_SCENARIOS_GROUPS: "simple_onboarding,simple_onboarding_profiling,simple_onboarding_appsec,docker-ssi,lib-injection"
 
 create_key:
diff --git a/tooling/update_system_test_reference.sh b/tooling/update_system_test_reference.sh
index 9271a414e83..769d61a40f6 100755
--- a/tooling/update_system_test_reference.sh
+++ b/tooling/update_system_test_reference.sh
@@ -14,8 +14,8 @@ fi
 GITHUB_TARGET=".github/workflows/run-system-tests.yaml"
 GITLAB_TARGET=".gitlab-ci.yml"
 GITHUB_PATTERN_1='(\s*system-tests\.yml@)(\S+)(\s+# system tests.*)' # pattern to update the "system-tests.yml@" reference
-GITHUB_PATTERN_2='(\s*ref: )(\S+)(\s+# system tests.*)' # pattern to update the "ref:" reference
-GITLAB_PATTERN='(\s*SYSTEM_TESTS_REF:\s*)(\S+)(\s+# system tests.*)' # pattern to update the GitLab SYSTEM_TESTS_REF variable
+GITHUB_PATTERN_2='(\s*ref: ")([^"]+)("\s+# system tests.*)' # pattern to update the quoted "ref:" reference
+GITLAB_PATTERN='(\s*SYSTEM_TESTS_REF: ")([^"]+)("\s+# system tests.*)' # pattern to update the quoted GitLab SYSTEM_TESTS_REF variable
 
 echo "Fetching latest commit SHA for system-tests branch: $BRANCH"
 REF=$(git ls-remote https://github.com/DataDog/system-tests "refs/heads/$BRANCH" | cut -f 1)