The Venturer also sank U771 which was not submerged while being hit by torpedoes.
This is wikipedia info, but apparently the British also used submarines for ASW. They seem to have lured in places where retreating/coming out of port, and would not be detected by passing submerged submarines.
Alas, let us consider which other wars might have seen submarine vs submarine action. Post WWII, technological development meant that submarines spent most of their time submerged, thus naval action in which at least one submarine was surfaced is unlikely.
Pre WWI, submarines were not really widespread, so the chances of both sides in a conflict having access to submarines are slim. In what wars could they have been involved?
In the American Secession War, both sides used submarines, but they were generally unfit for service and saw little action.
In the Russo-Japanese War, both sides had submarines, but wikipedia states that Japanese subs never saw action.
Balkan wars? Greece and Ottoman Empire might have had submarines.
During WWI, the Entente powers developed ASW submarines, but they came too late and saw no action.
Thus, I conclude, sub vs sub action is most likely found during WWII and nowhen else.
EDIT: During WW1, Italian submarine F-12 sunk Austrio-Hungarian submarine U-20. I admire the effort people put in some wikipedia articles.