Index: lib/Frontend/CompilerInvocation.cpp
===================================================================
--- lib/Frontend/CompilerInvocation.cpp
+++ lib/Frontend/CompilerInvocation.cpp
@@ -2988,8 +2988,9 @@
       return IntrusiveRefCntPtr<vfs::FileSystem>();
     }
 
-    IntrusiveRefCntPtr<vfs::FileSystem> FS = vfs::getVFSFromYAML(
-        std::move(Buffer.get()), /*DiagHandler*/ nullptr, File);
+    IntrusiveRefCntPtr<vfs::FileSystem> FS =
+        vfs::getVFSFromYAML(std::move(Buffer.get()), /*DiagHandler*/ nullptr,
+                            File, /*DiagContext*/ nullptr, BaseFS);
     if (!FS.get()) {
       Diags.Report(diag::err_invalid_vfs_overlay) << File;
       return IntrusiveRefCntPtr<vfs::FileSystem>();
Index: lib/Tooling/Tooling.cpp
===================================================================
--- lib/Tooling/Tooling.cpp
+++ lib/Tooling/Tooling.cpp
@@ -280,6 +280,12 @@
     Invocation->getPreprocessorOpts().addRemappedFile(It.getKey(),
                                                       Input.release());
   }
+  IntrusiveRefCntPtr<vfs::FileSystem> VirtualFileSystem =
+      createVFSFromCompilerInvocation(*Invocation, Diagnostics,
+                                      Files->getVirtualFileSystem());
+  if (Files->getVirtualFileSystem() != VirtualFileSystem) {
+    Files = new FileManager(Invocation->getFileSystemOpts(), VirtualFileSystem);
+  }
   return runInvocation(BinaryName, Compilation.get(), std::move(Invocation),
                        std::move(PCHContainerOps));
 }
Index: unittests/Tooling/ToolingTest.cpp
===================================================================
--- unittests/Tooling/ToolingTest.cpp
+++ unittests/Tooling/ToolingTest.cpp
@@ -21,6 +21,7 @@
 #include "llvm/Support/Path.h"
 #include "llvm/Support/TargetRegistry.h"
 #include "llvm/Support/TargetSelect.h"
+#include "llvm/Support/FormatVariadic.h"
 #include "gtest/gtest.h"
 #include <algorithm>
 #include <string>
@@ -171,6 +172,37 @@
   EXPECT_TRUE(Invocation.run());
 }
 
+TEST(ToolInvocation, TestVfsOverlay) {
+  llvm::IntrusiveRefCntPtr<vfs::OverlayFileSystem> OverlayFileSystem(
+      new vfs::OverlayFileSystem(vfs::getRealFileSystem()));
+  llvm::IntrusiveRefCntPtr<vfs::InMemoryFileSystem> InMemoryFileSystem(
+      new vfs::InMemoryFileSystem);
+  OverlayFileSystem->pushOverlay(InMemoryFileSystem);
+  llvm::IntrusiveRefCntPtr<FileManager> Files(
+      new FileManager(FileSystemOptions(), OverlayFileSystem));
+  std::vector<std::string> Args;
+  Args.push_back("tool-executable");
+  Args.push_back("-ivfsoverlay");
+  Args.push_back("overlay.yaml");
+  Args.push_back("-fsyntax-only");
+  Args.push_back("a.cpp");
+  clang::tooling::ToolInvocation Invocation(Args, new SyntaxOnlyAction,
+                                            Files.get());
+  InMemoryFileSystem->addFile(
+      "a.cpp", 0,
+      llvm::MemoryBuffer::getMemBuffer("#include <unknown_header>\n"));
+  std::string OverlayContent = llvm::formatv(
+      "{{'version': 0,'roots':[{{'name':'{0}','type':'directory',"
+	  "'contents':[{{'name':'a.cpp','type':'file',"
+	  "'external-contents':'b.cpp'}]}]}",
+      InMemoryFileSystem.get()->getCurrentWorkingDirectory().get());
+  InMemoryFileSystem->addFile("overlay.yaml", 0,
+                              llvm::MemoryBuffer::getMemBuffer(OverlayContent));
+  InMemoryFileSystem->addFile(
+      "b.cpp", 0, llvm::MemoryBuffer::getMemBuffer("int main() {}"));
+  EXPECT_TRUE(Invocation.run());
+}
+
 TEST(ToolInvocation, TestVirtualModulesCompilation) {
   // FIXME: Currently, this only tests that we don't exit with an error if a
   // mapped module.map is found on the include path. In the future, expand this