The 22ft long, eight-tonne male calf, which was probably under a year old and still suckling, was examined by vets from the Hebridean Whale and Dolphin Trust (HWDT) and Scotland's Rural College.
It was the first time a post-mortem examination had been carried out on a humpback in Scotland. HWDT said the results pointed to the animal being entangled underneath the salmon pen nets at Fishnish off Mull and drowned.
Nicola Hodgins, head of science and research at Whale and Dolphin Conservation, said: "This is incredibly sad news. This young whale would have suffocated through lack of oxygen and would have suffered and died in pain. As it was a very young whale, its mother would probably have been close by and it would have been incredibly traumatic for her as well. She may have been trying to move the calf from under the net."
She added: "It's very rare to see a humpback whale around the UK and for a young one to die in such a way is tragic."
The calf was found by fish farm staff on June 26 and workers from a nearby freight company used a crane to retrieve the animal's body from the water the following day.
Andrew Brownlow, veterinary pathologist at Scotland's Rural College, carried out the four-hour post-mortem examination on the dock where the dead calf was pulled out.
He said: "It is obviously very unfortunate when marine animals become entangled in this way, but it is thankfully still a relatively rare occurrence. We are still running tests on this case to investigate if there was any underlying reason which could explain this quite unusual behaviour.
"However, it is possible this was simply a young, inquisitive, maybe hungry animal who took a wrong turning."
There have only been six recorded humpback whale strandings in Scotland since 1992 and 17 for the whole of the UK.
The whale's stomach lining suggested little solid food had been ingested in the past, so it was possible that it was still receiving milk from its mother.
Male humpback whales often grow to around 48ft and can weigh up to 30 tonnes.
They are identified from other species of whales due to their large flippers, almost one-third of their body size, the hump on their backs and their knobbly head.
They are grey or black in colour and have white markings on their underside which differ in every whale. The markings allow researchers to identify individuals.
Humpback whales are also known for their water acrobatics and can been seen leaping out of the water. Males produce a complex song lasting 10 to 20 minutes, which they repeat for hours at a time. Its purpose is not clear, though it may have a role in mating.
Like other large whales, the humpback was and remains a target for the whaling industry. Once hunted to the brink of extinction, its population fell by an estimated 90 per cent before a moratorium was introduced in 1966. More than 400 marine mammals are stranded around the coast of Scotland every year.