Has a submerged submarine ever torpedoed another submerged submarine?

This happened almost exactly 60 years ago, on the 9th February 1945, when HMS Venturer sank U-864. With the fall of France, the German U-boat force had rebased to Norway and Northwestern Germany. Allied aircraft, submarines and escorts deployed to the North Sea to stop them sortieing into the North Atlantic.

U-864 was a Type IX U-boat. As part of Operation Ceasar, she attempted to run this blockade, carrying a load of jet engine parts, mercury and similar strategic materials to Japan. The British U-class submarine HMS Venturer was deployed to the coast of Norway, with orders to sink U-864. U-864 managed to avoid Venturer on her first sortie, but had to turn around and return to Bergen due to engine trouble. As she was returning, submerged due to the air threat, Venturer detected her by hydrophone. Venturer's captain spotted U-864's snorkel, and began to stalk the submerged submarine, hoping that she'd surface. It is possible that U-864 was aware of Venturer's presence, as she made several erratic maneuvers. After three hours of stalking, it was decided by Venturer's captain to fire a spread of torpedoes across the likely path of U-864. Four torpedoes were launched, based on a manual calculation of U-864's expected position. U-864 detected the launch and took evasive action. This meant that she avoided three of the torpedoes, but took her directly into the path of the fourth. The impact and detonation tore U-864 in half, sinking her with all hands.

This sinking is even more notable because it was carried out with unguided torpedoes. Many of the submarine movies you mention use Cold War technology. This allowed torpedoes to be guided directly to a target, instead of having to be blind-fired. However, due to the strategic realities of the Cold War, these haven't been used in anger.

Sources:

British Submarines 1939-45, Innes McCartney, Osprey, 2006

Nelson to Vanguard: Warship design and development 1923-1945, D. K. Brown, Seaforth, 2012