The 63-year-old was taken to the Southern General Hospital in Glasgow by air ambulance after the accident on the Isle of Bute on Saturday. He died yesterday morning.
A 52-year-old man, who was also on board, was airlifted to the Royal Alexandra Hospital in Paisley and remains in a critical condition.
The crash happened between the Kingarth and Kilchattan Bay areas at the south of the island at 3.45pm on Saturday.
Unconfirmed reports said the plane had been crop-dusting and came down about half-a-mile from the Kingarth airstrip.
It is also believed the plane was a Strathaven-based Sportscruiser.
Police Scotland are working with the Air Accidents Investigation Branch to investigate the crash.
Officers have appealed for witnesses, and would like to obtain any video or mobile phone footage.
The man's relatives have been informed of his death and a report will be submitted to the procurator-fiscal.
The Scottish Fire and Rescue Service said it received several calls about the crash.
It sent two fire tenders from Rothesay on the island and one from Tighnabruaich on the mainland.
Police said a part of the A844 West Road had to remain closed overnight.
Officers working on the investigation are urging any witnesses to contact them, and would like to obtain video or mobile phone footage which may help with their inquiry.
News of the crash has startled locals, who paid their respects on social network sites.
Karen Young of Rothesay said: "Heartbreaking, thoughts are with his family and friends. RIP. X."
Michael Steven of Port Bannatyne added: "My thoughts are with the family and the surviving man, hope he is able to make a full recovery."
The accident came seven weeks after a "full emergency" situation was declared at Bute's airstrip after the pilot of a light aircraft in the area reported engine difficulties.
The pilot told air traffic controllers they were experiencing "unusual vibrations" from his plane's engine, and was diverted to the Baird Airstrip at Kingarth, the nearest available landing area.
Police in Rothesay were alerted and headed to the airfield, while the RAF was also kept aware of developments.
In the end, the pilot was able to land his aircraft safely at Kingarth some 10 minutes after the alert was given out.