You can use the output clause from the merge statement into a temp table then filter the results and add them into your third table.
Example of Merge Output
-----Inserting data when no match found.
MERGE [dbo].[Department_Target] AS tar
USING [dbo].[Department_Source] AS src
ON tar.[DepartmentID] = src.[DepartmentID]
WHEN NOT MATCHED THEN
INSERT
(
[DepartmentID],
[Name],
[GroupName],
[ModifiedDate]
)
VALUES
(
src.[DepartmentID], src.[Name], src.[GroupName], src.[ModifiedDate]
)
OUTPUT
$action,
inserted.*,
deleted.*;