Supergirl accidentally kills Krypto with Fatal Vision.
Fatal Vision was a power supposedly granted by Red Kryptonite in a delusion which was, itself, induced upon Supergirl by Red Kryptonite. Fatal vision allows Supergirl to kill any being simply by looking at them, even Kryptonians. Also, the vision could not be turned off, so even a glance could kill. In the delusion, Supergirl killed several people this way, including the Danvers, her foster parents, and Krypto. ("The Strange Bodies of Supergirl!")