Allows a user to save a prefab in play mode.

SavePrefab.cs

using UnityEngine;
using System.Collections;

public class SavePrefab : MonoBehaviour {

}

SavePrefabEditor.cs

using UnityEngine;
using UnityEditor;
using System.Collections;

[CustomEditor(typeof(SavePrefab))]
public class SavePrefabEditor : Editor {

    public override void OnInspectorGUI(){
        SavePrefab saveTarget = target as SavePrefab;
        if( GUILayout.Button("Save") ){
            Object parentObject = PrefabUtility.GetPrefabParent(saveTarget.gameObject);
            if( parentObject == null ){
                Debug.LogWarningFormat("No prefab found for GameObject {0}",saveTarget.gameObject.name);
                return;
            }
            PrefabUtility.ReplacePrefab( saveTarget.gameObject, parentObject );
            AssetDatabase.SaveAssets();
        }

    }
}