Consider the commonjs module indicator as a module indicator

src/compiler/transformers/module/module.ts

@@ -56,7 +56,7 @@ namespace ts {
          * @param node The SourceFile node.
          */
         function transformSourceFile(node: SourceFile) {
-            if (node.isDeclarationFile || !(isExternalModule(node) || compilerOptions.isolatedModules || node.transformFlags & TransformFlags.ContainsDynamicImport)) {
+            if (node.isDeclarationFile || !(isEffectiveExternalModule(node, compilerOptions) || node.transformFlags & TransformFlags.ContainsDynamicImport)) {
                 return node;
             }
 

src/compiler/utilities.ts

@@ -444,7 +444,7 @@ namespace ts {
     }
 
     export function isEffectiveExternalModule(node: SourceFile, compilerOptions: CompilerOptions) {
-        return isExternalModule(node) || compilerOptions.isolatedModules;
+        return isExternalModule(node) || compilerOptions.isolatedModules || ((getEmitModuleKind(compilerOptions) === ModuleKind.CommonJS) && !!node.commonJsModuleIndicator);
     }
 
     /* @internal */

tests/baselines/reference/javascriptCommonjsModule.js

@@ -0,0 +1,23 @@
+//// [index.js]
+class Foo {}
+
+class Bar extends Foo {}
+
+module.exports = Bar;
+
+
+//// [index.js]
+var tslib_1 = require("tslib");
+var Foo = /** @class */ (function () {
+    function Foo() {
+    }
+    return Foo;
+}());
+var Bar = /** @class */ (function (_super) {
+    tslib_1.__extends(Bar, _super);
+    function Bar() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return Bar;
+}(Foo));
+module.exports = Bar;

tests/baselines/reference/javascriptCommonjsModule.symbols

@@ -0,0 +1,13 @@
+=== tests/cases/compiler/index.js ===
+class Foo {}
+>Foo : Symbol(Foo, Decl(index.js, 0, 0))
+
+class Bar extends Foo {}
+>Bar : Symbol(Bar, Decl(index.js, 0, 12))
+>Foo : Symbol(Foo, Decl(index.js, 0, 0))
+
+module.exports = Bar;
+>module : Symbol(export=, Decl(index.js, 2, 24))
+>exports : Symbol(export=, Decl(index.js, 2, 24))
+>Bar : Symbol(Bar, Decl(index.js, 0, 12))
+

tests/baselines/reference/javascriptCommonjsModule.types

@@ -0,0 +1,15 @@
+=== tests/cases/compiler/index.js ===
+class Foo {}
+>Foo : Foo
+
+class Bar extends Foo {}
+>Bar : Bar
+>Foo : Foo
+
+module.exports = Bar;
+>module.exports = Bar : typeof Bar
+>module.exports : any
+>module : any
+>exports : any
+>Bar : typeof Bar
+

tests/cases/compiler/javascriptCommonjsModule.ts

@@ -0,0 +1,11 @@
+// @allowJS: true
+// @outDir: ./out
+// @module: commonjs
+// @noEmitHelpers: true
+// @importHelpers: true
+// @filename: index.js
+class Foo {}
+
+class Bar extends Foo {}
+
+module.exports = Bar;