diff --git a/src/cargo/core/compiler/custom_build.rs b/src/cargo/core/compiler/custom_build.rs
index d7e6aadc306..369b048dfe2 100644
--- a/src/cargo/core/compiler/custom_build.rs
+++ b/src/cargo/core/compiler/custom_build.rs
@@ -469,20 +469,10 @@ fn build_work(build_runner: &mut BuildRunner<'_, '_>, unit: &Unit) -> CargoResul
             if dep.unit.mode.is_run_custom_build() {
                 let dep_metadata = build_runner.get_run_build_script_metadata(&dep.unit);
 
-                let Some(dependency) = unit.pkg.dependencies().iter().find(|d| {
-                    d.package_name() == dep.unit.pkg.name()
-                        && d.source_id() == dep.unit.pkg.package_id().source_id()
-                        && d.version_req().matches(dep.unit.pkg.version())
-                }) else {
-                    panic!(
-                        "Dependency `{}` not found in `{}`s dependencies",
-                        dep.unit.pkg.name(),
-                        unit.pkg.name()
-                    )
-                };
+                let dep_name = dep.dep_name.unwrap_or(dep.unit.pkg.name());
 
                 Some((
-                    dependency.name_in_toml(),
+                    dep_name,
                     dep.unit
                         .pkg
                         .manifest()
diff --git a/src/cargo/core/compiler/unit_dependencies.rs b/src/cargo/core/compiler/unit_dependencies.rs
index 7b9e6426ab5..113a3d1f2d4 100644
--- a/src/cargo/core/compiler/unit_dependencies.rs
+++ b/src/cargo/core/compiler/unit_dependencies.rs
@@ -1005,7 +1005,16 @@ fn connect_run_custom_build_deps(state: &mut State<'_, '_>) {
                     state.unit_dependencies[&other.unit]
                         .iter()
                         .find(|other_dep| other_dep.unit.mode == CompileMode::RunCustomBuild)
-                        .cloned()
+                        .map(|other_dep| {
+                            let mut dep = other_dep.clone();
+                            let dep_name = other.dep_name.unwrap_or(other.unit.pkg.name());
+                            // Propagate the manifest dep name from the sibling edge.
+                            // The RunCustomBuild-RustCustomBuild edge is synthetic
+                            // and doesn't carry a usable dep name, but build script
+                            // metadata needs one for `CARGO_DEP_<dep_name>_*` env var
+                            dep.dep_name = Some(dep_name);
+                            dep
+                        })
                 })
                 .collect::<HashSet<_>>();
 
diff --git a/src/cargo/core/compiler/unit_graph.rs b/src/cargo/core/compiler/unit_graph.rs
index fa1fae48001..40e2d660e52 100644
--- a/src/cargo/core/compiler/unit_graph.rs
+++ b/src/cargo/core/compiler/unit_graph.rs
@@ -26,11 +26,15 @@ pub struct UnitDep {
     pub unit_for: UnitFor,
     /// The name the parent uses to refer to this dependency.
     pub extern_crate_name: InternedString,
-    /// If `Some`, the name of the dependency if renamed in toml.
-    /// It's particularly interesting to artifact dependencies which rely on it
-    /// for naming their environment variables. Note that the `extern_crate_name`
-    /// cannot be used for this as it also may be the build target itself,
-    /// which isn't always the renamed dependency name.
+    /// The dependency name as written in the manifest (including a rename).
+    ///
+    /// `None` means this edge does not carry a manifest dep name. For example,
+    /// std edges in build-std or synthetic edges for build script executions.
+    /// When `None`, the package name is typically used by callers as a fallback.
+    ///
+    /// This is mainly for Cargo-synthesized outputs
+    /// (artifact env vars and `CARGO_DEP_*` metadata env)
+    /// and is distinct from `extern_crate_name`.
     pub dep_name: Option<InternedString>,
     /// Whether or not this is a public dependency.
     pub public: bool,
diff --git a/tests/testsuite/build_script.rs b/tests/testsuite/build_script.rs
index 190158a3078..a185384feb0 100644
--- a/tests/testsuite/build_script.rs
+++ b/tests/testsuite/build_script.rs
@@ -1722,6 +1722,54 @@ fn non_links_can_pass_env_vars_direct_deps_only() {
         .run();
 }
 
+/// Regression test for https://github.com/rust-lang/cargo/issues/16493
+#[cargo_test]
+fn with_patch() {
+    Package::new("cxx", "1.0.0").publish();
+
+    let p = project()
+        .file(
+            "Cargo.toml",
+            r#"
+            [package]
+            name = "foo"
+            edition = "2021"
+
+            [dependencies]
+            cxx = "1.0.0"
+
+            [patch.crates-io]
+            cxx = { path = "cxx" }
+            "#,
+        )
+        .file("src/lib.rs", "")
+        .file("build.rs", "fn main() {}")
+        .file(
+            "cxx/Cargo.toml",
+            r#"
+            [package]
+            name = "cxx"
+            version = "1.0.0"
+            edition = "2021"
+            links = "cxx"
+            "#,
+        )
+        .file("cxx/src/lib.rs", "")
+        .file("cxx/build.rs", "fn main() {}")
+        .build();
+
+    p.cargo("check")
+        .with_stderr_data(str![[r#"
+[UPDATING] `dummy-registry` index
+[LOCKING] 1 package to latest compatible version
+[COMPILING] cxx v1.0.0 ([ROOT]/foo/cxx)
+[COMPILING] foo v0.0.0 ([ROOT]/foo)
+[FINISHED] `dev` profile [unoptimized + debuginfo] target(s) in [ELAPSED]s
+
+"#]])
+        .run();
+}
+
 #[cargo_test]
 fn only_rerun_build_script() {
     let p = project()