diff --git a/git_drover.py b/git_drover.py
index ad6d0e13c..c9a4af315 100755
--- a/git_drover.py
+++ b/git_drover.py
@@ -265,8 +265,9 @@ class _Drover(object):
     repo_status = self._run_git_command(['status', '--porcelain']).splitlines()
     extra_files = [f[3:] for f in repo_status if f[:2] == ' D']
     if extra_files:
-      self._run_git_command(['update-index', '--skip-worktree', '--'] +
-                            extra_files)
+      self._run_git_command_with_stdin(
+          ['update-index', '--skip-worktree', '--stdin'],
+          stdin='\n'.join(extra_files) + '\n')
 
   def _upload_and_land(self):
     if self._dry_run:
@@ -314,6 +315,32 @@ class _Drover(object):
       else:
         raise Error('Command %r failed: %s' % (' '.join(args), e))
 
+  def _run_git_command_with_stdin(self, args, stdin):
+    """Runs a git command with a provided stdin.
+
+    Args:
+      args: A list of strings containing the args to pass to git.
+      stdin: A string to provide on stdin.
+
+    Raises:
+      Error: The command failed to complete successfully.
+    """
+    cwd = self._workdir if self._workdir else self._parent_repo
+    logging.debug('Running git %s (cwd %r)', ' '.join('%s' % arg
+                                                      for arg in args), cwd)
+
+    # Discard stderr unless verbose is enabled.
+    stderr = None if self._verbose else _DEV_NULL_FILE
+
+    try:
+      popen = subprocess.Popen(['git'] + args, shell=False, cwd=cwd,
+                               stderr=stderr, stdin=subprocess.PIPE)
+      popen.communicate(stdin)
+      if popen.returncode != 0:
+        raise Error('Command %r failed' % ' '.join(args))
+    except OSError as e:
+      raise Error('Command %r failed: %s' % (' '.join(args), e))
+
 
 def cherry_pick_change(branch, revision, parent_repo, dry_run, verbose=False):
   """Cherry-picks a change into a branch.
diff --git a/tests/git_drover_test.py b/tests/git_drover_test.py
index 98f9352ed..ea38df600 100755
--- a/tests/git_drover_test.py
+++ b/tests/git_drover_test.py
@@ -37,6 +37,8 @@ class GitDroverTest(auto_stub.TestCase):
     self.mock(__builtins__, 'raw_input', self._get_input)
     self.mock(subprocess, 'check_call', self._check_call)
     self.mock(subprocess, 'check_output', self._check_call)
+    self.real_popen = subprocess.Popen
+    self.mock(subprocess, 'Popen', self._Popen)
     self._commands = []
     self._input = []
     self._fail_on_command = None
@@ -75,7 +77,7 @@ class GitDroverTest(auto_stub.TestCase):
       ]
     self.MANUAL_RESOLVE_PREPARATION_COMMANDS = [
         (['git', 'status', '--porcelain'], self._target_repo),
-        (['git', 'update-index', '--skip-worktree', '--', 'foo', 'bar'],
+        (['git', 'update-index', '--skip-worktree', '--stdin'],
          self._target_repo),
     ]
     self.FINISH_MANUAL_RESOLVE_COMMANDS = [
@@ -113,6 +115,25 @@ class GitDroverTest(auto_stub.TestCase):
       return ' D foo\nUU baz\n D bar\n'
     return ''
 
+  def _Popen(self, args, shell=False, cwd=None, stdin=None, stdout=None,
+             stderr=None):
+    if args == ['git', 'update-index', '--skip-worktree', '--stdin']:
+      self._commands.append((args, cwd))
+      self.assertFalse(shell)
+      self.assertEqual(stdin, subprocess.PIPE)
+      class MockPopen(object):
+        def __init__(self, *args, **kwargs):
+          self.returncode = -999
+        def communicate(self, stdin):
+          if stdin == 'foo\nbar\n':
+            self.returncode = 0
+          else:
+            self.returncode = 1
+      return MockPopen()
+    else:
+      return self.real_popen(args, shell=shell, cwd=cwd, stdin=stdin,
+                             stdout=stdout, stderr=stderr)
+
   def testSuccess(self):
     self._input = ['y', 'y']
     git_drover.cherry_pick_change('branch', 'cl', self._parent_repo, False)