I have implemented deep linking in my app. I added this intent filter in my manifest file, and the deep linking is working.
You need to do following things for your Activity in your Manifest.
android:launchMode="singleTask"
This tells the system to always launch the existing instance of the Activity if it is already created.
And you can handle the Intent then by overriding the method
onNewIntent
See http://developer.android.com/guide/topics/manifest/activity-element.html for more information.