He announced the price of petrol and diesel would go up more than 30 percent from midnight, a deep cut to government subsidies that will be welcomed by economists but risks denting the new president's popularity.
"From time to time, a nation faces difficult choices -- nevertheless, we must take a decision," the president, known as Jokowi, said in a televised address to the nation.
Government fuel subsidies are a thorny issue in Indonesia. Economists have long been calling for the payouts that gobble up a huge chunk of the state budget to be reduced but large sections of the public are staunchly against any increase.
However most parts of the county were calm before the announcement, which had been expected for weeks, and TV news channels focused their attention on queues of cars and motorcyclists waiting to fill up on cheap fuel before midnight.
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Analysts hailed the move by Widodo, who took office last month, as it fulfilled a campaign pledge to cut the payouts in order to divert money to reforms, such as overhauling infrastructure and helping the country's poorest.
"The move is encouraging since it suggests that Jokowi is serious about economic reform in Indonesia, and is even prepared to take steps that may prove unpopular in the short-run," said Gareth Leather, Asia economist from Capital Economics.
The price of petrol is rising 2,000 rupiah (16 US cents) to 8,500 a litre, a increase of just over 30 percent, while diesel will go up 2,000 rupiah to 7,500 a litre, a 35 percent increase, Widodo said late today.
Widodo, Indonesia's first leader from outside the political and military elites, also said there would be "social protection" for the poorest, a reference to a government scheme aimed at providing cash handouts to cushion the impact of the fuel price increase.
The cut in subsidies was smaller than some had been expected after recent steep falls in global oil prices granted the government some breathing space as it's fuel import bill shrank.