diff --git a/uv/lib/dependabot/uv/file_updater/lock_file_updater.rb b/uv/lib/dependabot/uv/file_updater/lock_file_updater.rb
index 0dc0a47d7e9..5f2bf647cec 100644
--- a/uv/lib/dependabot/uv/file_updater/lock_file_updater.rb
+++ b/uv/lib/dependabot/uv/file_updater/lock_file_updater.rb
@@ -96,10 +96,15 @@ def fetch_updated_dependency_files
           updated_files = pyproject_files.filter_map do |file|
             next unless file_changed?(file)
 
-            updated_file(
+            updated = updated_file(
               file: file,
               content: T.must(updated_pyproject_content_for(file))
             )
+            # support_file must be false to prevent DependencyChangeBuilder from discarding the inner TOML,
+            # since doing so causes a conflict between the updated lock file and the committed TOML
+            # and breaks `uv sync --locked` in CI.
+            updated.support_file = false
+            updated
           end
 
           if lockfile && !build_system_only_dependency?
diff --git a/uv/spec/dependabot/uv/file_updater/lock_file_updater_spec.rb b/uv/spec/dependabot/uv/file_updater/lock_file_updater_spec.rb
index 3df6e0c7d23..270bd79ecb2 100644
--- a/uv/spec/dependabot/uv/file_updater/lock_file_updater_spec.rb
+++ b/uv/spec/dependabot/uv/file_updater/lock_file_updater_spec.rb
@@ -479,6 +479,7 @@
 
         member_pyproject = updated_dependency_files.find { |f| f.name == "packages/my-package/pyproject.toml" }
         expect(member_pyproject.content).to include('"click>=8.2.0"')
+        expect(member_pyproject.support_file).to be(false)
 
         updated_lock = updated_dependency_files.find { |f| f.name == "uv.lock" }
         expect(updated_lock.content).to include('version = "8.2.0"')