Kerry will also travel to Manila for talks with Philippine officials, according to the U.S. Embassy there.
Obama was to have been the first U.S. president to visit Malaysia since Lyndon B. Johnson in 1966.
"I empathize and understand," Najib said of Obama's decision to cancel. "If I were in his shoes, I would do the same."
In Manila, Ricky Carandang, a spokesman for Aquino, also said that Obama's decision was understandable, and that the Philippines looks forward to welcoming him "at a more opportune time."
The Philippine Department of Foreign Affairs said in a statement that relations between the two countries "remain strong and forward-looking."
The shutdown took effect Tuesday after Congress missed its deadline to fund the government.
Obama twice canceled trips to Asia in 2010, once to stay in Washington for votes on his health care law, and once because of an oil spill in the Gulf of Mexico.