The largest economy in Southeast Asia saw its general price level, as measured by the consumer price index (CPI), grow by only 2.19 percent last month compared to the same month a year earlier.
The last time Indonesia saw lower inflation was in June 2000, according to data compiled by the Inflation.eu website.
Inflation in the country has continuously slowed this year, with a reading of 2.67 percent in April.
"Inflation slowed down in May. This was unusual compared to the previous years, especially during Ramadan and Idul Fitri," Suhariyanto, the head of the Central Statistics Agency, said in a statement on Tuesday.
The Islamic fasting month and the festivities following it are usually times when Muslims spend big on food and new clothes.
But this year, the Covid-19 pandemic had forced shops and markets to close, which meant many people could not do their normal Idul Fitri shopping.
Suhariyanto said prices of staple food such as fish, chicken, beef and onion fell in May compared to the previous month.
Meanwhile, Bank Indonesia, the country's central bank, has kept its benchmark interest rate at 4.5 percent for the past three months.
Bank Indonesia said consistently lower inflation will leave room for further rate cuts.
The central bank expects inflation to hover between 2 percent and 4 percent this year.