The deep-diving species whales are rarely seen at sea and can spend long periods underwater hunting squid and fish.
One stranded at Ardersier, east of Inverness, and was found on Tuesday evening.
Efforts were made by British Divers Marine Life Rescue volunteers, coastguard personnel and Scottish Marine Animal Stranding Scheme (SMASS) vet Andrew Brownlow to save the whale.
The second whale was found last Wednesday, more than 20 miles away from the first at Culbin near Findhorn.
SMASS said an examination of this animal suggested it had also stranded alive the same day as the Ardersier whale.
It said both animals had died due to long times spent stranded, and had suffered organ damage.
According to the charity Whale and Dolphin Conservation, Sowerby's beaked whales were the first of beaked whale species to be discovered after a stranding in the Moray Firth in 1800.