You can't. As far as search is concerned, both tags mean the same thing.
Having a tag synonym where some questions are actually still tagged with the synonym is meant to be a temporary state, and a short one at that. It's an option to see how the synonym goes over without completing the irreversible action of a full merge (allows a moderator easily remove the synonym and go back to two independent tags with minimal effort). At some point, the tags should also be merged so they are all using one tag if the synonym hasn't caused any problems.
The only valid solutions to a search for one tag returning questions with that tag and its synonyms:
- Simply remove the synonym tag from the question if it shouldn't be there.
- Remove the synonym if it's not actually valid.
- Get a moderator to merge the two tags fully if they mean the same thing.
Being able to explicitly search for a tag minus a synonym is not something we'll support because it's not a situation that should exist. If it's causing a problem, then the process broke down somewhere else and should be fixed there.