Shin had been in charge since 2020 and took Indonesia into the decisive third round of qualifying, where they sit third out of six teams in their group.
The top two go straight to the World Cup with third and fourth going into another round of qualifying.
Erick Thohir, chairman of the Football Association of Indonesia (PSSI), said the 54-year-old had been sacked because of communication issues and poor recent performances.
Indonesia have already hired a replacement from Europe and he will be introduced to the public on Sunday, Thohir said.
"Coach Shin Tae-yong has received the paperwork and there will be further process on our ending partnership," Thohir told a press conference.
"Once again I'd like to thank him."
Indonesia, who have naturalised a dozen players born in the Netherlands, lost 2-1 at home to China and then were thrashed 4-0 by Japan in November in qualifying for the World Cup in North America.
They then defeated Saudi Arabia 2-0 in Jakarta and remain firmly in with a shout of qualifying for the competition for the first time since the country gained independence in 1945.
Shin, who managed his native South Korea at the 2018 World Cup, had been contracted until 2027.
Indonesia's next World Cup qualifier is a crunch trip to Australia, who are second in the group but just a point ahead, in March.
