The lauded London-born ecologist and botanist, who was not terminally ill, said the decision had been driven by his deteriorating quality of life.
Mr Goodall had flown from Australia for his assisted suicide, attracting the attention of people around the world.
Shortly before his death, he said he was "happy to end" his life.
"My life has been rather poor for the past year or so and I'm very happy to end it," he said, surrounded by several family members.
"All the publicity that this has been receiving can only, I think, help the cause of euthanasia for the elderly, which I want."
The academic died "peacefully" at 10:30 GMT at the Life Cycle clinic in Basel, from an infusion of Nembutal, a barbiturate, said Philip Nitschke, founder of Exit International, the group which helped him take his own life.
He was visibly frustrated by the process of formal paperwork, and Mr Nitschke later said: "In fact his last words were 'This is taking an awfully long time!'"
Mr Goodall's last meal was his favourite - fish and chips and cheesecake - and in his final minutes he was played Ode to Joy from Beethoven's 9th symphony.
Mr Goodall had lived on his own in a small flat in Perth, Western Australia, until only a few weeks before his trip to Switzerland.
He stepped back from full-time employment in 1979, but remained heavily involved in his field of work.
Among his achievements in recent years, Mr Goodall edited a 30-volume book series called Ecosystems of the World and was made a Member of the Order of Australia for his scientific work.
In 2016, aged 102, he won a battle to keep working on campus at Perth's Edith Cowan University, where he was an unpaid honorary research associate.
Mr Goodall said he resented having to leave Australia to end his life. Assisted dying is legal in only one state, but eligibility requires a person to be terminally ill.
Meanwhile, Switzerland has allowed assisted suicide since 1942.
Mr Goodall arrived in Basel on Monday after visiting relatives in France, and spent his final full day exploring the Basel University botanic gardens with three of his grandchildren.
At a press conference on Wednesday, he said he was surprised by the public interest in his case. He said: "I no longer want to continue life.
"One wants to, at my age, even rather less than my age... to be free to choose death when the death is at an appropriate time."
He wanted no funeral and requested that his body be donated to medicine or his ashes sprinkled locally, Exit International said.
Assisted suicide describes any act that intentionally helps another person kill themselves, for example by providing them with the means to do so, most commonly by prescribing a lethal medication.
It differs from euthanasia, which is a third-party intervention to end a life to relieve suffering, such as when a doctor administers the lethal dose.