The blue-chip oil and gas group had a 51 per cent stake in Shell Refining Company. The business includes a 125,000 barrels per day refinery in Port Dickson, south of Kuala Lumpur.
Malaysia remains "an important market" for the company, Shell said in a statement.
The divestment is consistent with the group's strategy to "concentrate its global downstream operations in areas where it can be most competitive".
Ailing oil prices since 2014 have put huge pressure on oil and gas companies, forcing many to streamline their operations.
Shell said it will maintain supply to its retail and commercial customers and will honour all current commercial arrangements through existing comprehensive supply agreements in the country.
The company's share price was unmoved by the announcement, rising 0.2 per cent to 2,202p in late morning trading.