The line will connect the Indonesian capital Jakarta with the mountain-fringed city of Bandung, some 160 kilometres (100 miles) away, and is a key part of President Joko Widodo's plans to overhaul the archipelago's infrastructure and attract investors.
Japan was long expected to build the railway but China entered the contest earlier this year, and Tokyo's bid was rejected last month after a chaotic bidding process that infuriated the Japanese.
"This high-speed train will make it easier for the public to travel," he told reporters in Jakarta, where the deal was inked. "This major project will also provide major employment opportunities and boost the economy."
State-owned China Development Bank will provide 75 per cent of the funding, with the rest coming from the Chinese railway company and Indonesian consortium.
The high-speed train route will cover eight stations from Jakarta to Bandung, and the train will travel at around 250 kilometres (150 miles) an hour.
The Indonesian government repeatedly changed its mind about the railway project, before eventually agreeing to accept China's bid for a high-speed line.
The chaotic bidding process and final decision angered Tokyo, which is increasingly competing with Beijing for influence in Asia, with chief government spokesman Yoshihide Suga slamming it as "extremely regrettable".
China has built thousands of kilometres of high-speed railway in recent years, but its safety standards have come under scrutiny - a 2011 crash killed at least 40 people and injured about 200.
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