How do I prevent the status bar and navigation bar from animating during an activity scene animation transition?

There are two approaches you can use that I know of to prevent the navigation/status bar from animating during the transition:

Approach #1: Exclude the status bar and navigation bar from the window's default exit/enter fade transition

The reason why the navigation/status bar are fading in and out during the transition is because by default all non-shared views (including the navigation/status bar backgrounds) will fade out/in in your calling/called Activitys respectively once the transition begins. You can, however, easily get around this by excluding the navigation/status bar backgrounds from the window's default exit/enter Fade transition. Simply add the following code to your Activitys' onCreate() methods:

Transition fade = new Fade();
fade.excludeTarget(android.R.id.statusBarBackground, true);
fade.excludeTarget(android.R.id.navigationBarBackground, true);
getWindow().setExitTransition(fade);
getWindow().setEnterTransition(fade);

This transition could also be declared in the activity's theme using XML (i.e. in your own res/transition/window_fade.xml file):

<?xml version="1.0" encoding="utf-8"?>
<fade xmlns:android="http://schemas.android.com/apk/res/android">
    <targets>
        <target android:excludeId="@android:id/statusBarBackground"/>
        <target android:excludeId="@android:id/navigationBarBackground"/>
    </targets>
</fade>

Approach #2: Add the status bar and navigation bar as shared elements

This approach builds off of klmprt's answer, which almost worked for me... although I still needed to make a couple of modifications.

In my calling Activity, I used the following code to start the Activity:

View statusBar = findViewById(android.R.id.statusBarBackground);
View navigationBar = findViewById(android.R.id.navigationBarBackground);

List<Pair<View, String>> pairs = new ArrayList<>();
if (statusBar != null) {
  pairs.add(Pair.create(statusBar, Window.STATUS_BAR_BACKGROUND_TRANSITION_NAME));
}
if (navigationBar != null) {
  pairs.add(Pair.create(navigationBar, Window.NAVIGATION_BAR_BACKGROUND_TRANSITION_NAME));
}
pairs.add(Pair.create(mSharedElement, mSharedElement.getTransitionName()));

Bundle options = ActivityOptions.makeSceneTransitionAnimation(activity, 
        pairs.toArray(new Pair[pairs.size()])).toBundle();
startActivity(new Intent(context, NextActivity.class), options);

So far this is essentially the same thing that klmprt suggested in his answer. However, I also needed to add the following code in my called Activity's onCreate() method in order to prevent the status bar and navigation bar from "blinking" during the transition:

@Override
protected void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    setContentView(R.layout.activity_next);

    // Postpone the transition until the window's decor view has
    // finished its layout.
    postponeEnterTransition();

    final View decor = getWindow().getDecorView();
    decor.getViewTreeObserver().addOnPreDrawListener(new ViewTreeObserver.OnPreDrawListener() {
        @Override
        public boolean onPreDraw() {
            decor.getViewTreeObserver().removeOnPreDrawListener(this);
            startPostponedEnterTransition();
            return true;
        }
    });
}

Adding the status bar and navigation bar backgrounds as shared elements will force them to be drawn on top of the window's default exit/enter fade transition, meaning that they will not fade during the transition. More discussion about this approach can be found in this Google+ post.

Completely prevent Activity transitions from interfering with shared element transitions:

On the exiting activity, call getWindow().setExitTransition(null);

On the entering activity, call getWindow().setEnterTransition(null);

From https://stackoverflow.com/a/34907685/967131

I suspect this may have side effects, but don't know for sure. It is dead simple and works though.

Prevent specific elements from blinking:

I started with Alex Lockwood's answer and did a fair bit of experimentation to try to get it working. The core of it is correct, although I didn't need the code he suggests for the receiving Activity, but I ran into some problems by calling it in a Fragment (instead of an Activity) and by setting a toolbar as the action bar.

Oh, the Fragment thing? I saw a lot of comments that trying to retrieve references to the status bar and navigation bar were null. The same thing happened to me as well, until I realized I wouldn't find those in the Fragment's layout... they were above that level. Hence, the code below to get the decor view from the Activity and search that. Then I found them with no problem.

In the end, I developed this utility method:

public static Bundle transitionOptions(Activity activity, int transitionViewResId, int transitionNameResId) {
   if (VERSION.SDK_INT < VERSION_CODES.LOLLIPOP) {
       return null;
   }

   View decorView = activity.getWindow().getDecorView();
   View statusBar = decorView.findViewById(android.R.id.statusBarBackground);
   View navigationBar = decorView.findViewById(android.R.id.navigationBarBackground);
   View appBarLayout = decorView.findViewById(**R.id.appbarlayout**);
   View transitionView = decorView.findViewById(transitionViewResId);
   String transitionName = activity.getString(transitionNameResId);

   List<Pair<View, String>> pairs = new ArrayList<>();
   pairs.add(Pair.create(statusBar, Window.STATUS_BAR_BACKGROUND_TRANSITION_NAME));
   pairs.add(Pair.create(navigationBar, Window.NAVIGATION_BAR_BACKGROUND_TRANSITION_NAME));
   if (appBarLayout != null) {
       pairs.add(Pair.create(appBarLayout, activity.getString(**R.string.transition_appbarlayout**)));
   }
   pairs.add(Pair.create(transitionView, transitionName));
   //noinspection unchecked - we're not worried about the "unchecked" conversion of List<Pair> to Pair[] here
   return ActivityOptionsCompat.makeSceneTransitionAnimation(activity, pairs.toArray(new Pair[pairs.size()]))
           .toBundle();
}

Note R.string.transition_appbarlayout and R.id.appbarlayout. These IDs are arbitrary, as long as they match what your code uses. In my XML, I layout the custom action bar like so (edited down to the essentials):

<?xml version="1.0" encoding="utf-8"?>
<android.support.design.widget.AppBarLayout
    android:id="**@+id/appbarlayout**"
    android:transitionName="**@string/transition_appbarlayout**">

    <android.support.v7.widget.Toolbar
        android:id="@+id/toolbar"/>
</android.support.design.widget.AppBarLayout>

If you don't use a Toolbar like this, that part can be removed from the utility method.

Then you would call it in your Fragment like so:

startActivity(intent, UIUtils.transitionOptions(getActivity(),
                        R.id.**my_view**,
                        R.string.**transition_my_view**));

Using whatever values you want, as long as it matches your XML.

This prevents the status bar, the tool bar and the navigation bar (back / home / recent apps buttons) from flashing during the transition. The rest of the Activity transition is normal.

In my case, our app theme has a android:windowBackground of blue. This causes a blue flash in the transition, which is quite frustrating. But rather than make a change that affects the entire app like that, for now I am going with the first, quick and dirty option.

I just had this same issue, and the answers appear to be missing a critical piece to the puzzle. Remember that on a shared element transition, everything happens in the Destination Activity.

In order to remove the flashing effect, simply add the following to the activity being called:

Fade fade = new Fade();
fade.excludeTarget(android.R.id.statusBarBackground, true);
fade.excludeTarget(android.R.id.navigationBarBackground, true);

getWindow().setEnterTransition(fade);
getWindow().setExitTransition(fade);

This should solve your problem!