The announcement on Sunday follows a leave of absence by the head of state and rumours he had married a former Russian beauty queen.
The abdication of Sultan Muhammad V as Malaysia's head of state is the first in the history of the country.
The palace statement said the king, who took the throne in December 2016, was grateful for the opportunity given to him by the Council of Rulers and thanked the prime minister and government for their cooperation during his rule.
Sultan Muhammad V abdicated as the 15th Yang di-Pertuan Agong today.
Next in line is Sultan Ahmad Shah of Pahang, but he is said to be ailing and his son has been Regent for two years.
The rotating monarchy system has been in place since independence from Britain in 1957, and Sultan Muhammad V is the first monarch to have renounced the throne.
Media has also reported some tension between the palace and the government of Prime Minister Mahathir Mohamad since the veteran leader returned to power previous year.More news: Enes Kanter Won't Travel With Knicks to London Fearing for His Life
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Sultan Muhammad V delayed Mahathir's swearing-in as prime minister after a historic election victory in May previous year, and also delayed giving his consent to the appointment of a non-Muslim attorney general.
Photos circulating on social media showed the Sultan, 49, wearing a traditional Malaysian national tunic while the bride wore an elaborate white gown, and Islamic headscarf, decorated with crystals.
But it is largely ceremonial, with power in the hands of parliament and the prime minister.
Sultan Muhammad V of Malaysia saluting a royal guard of honour during the opening ceremony of the Parliament in Kuala Lumpur in July a year ago.
Officially, the King said he was on medical leave.
The third sultan who was not present was King Muhammad.
But there had been growing unease after reports emerged in foreign media in late November - several weeks after the king went on leave - that he had married the Russian, Oksana Voevodina.
In June, the government and palace faced a near two-week impasse over a plan to appoint a non-Malay as attorney-general.