Muhammad Afrizal, 30, was rushed to hospital on Friday, an hour after losing a 12-round bout against countryman Irvan Marbun, in which he was knocked out and lost on points.
The former Pan Asia Boxing Association featherweight champion began vomiting soon after the end of the junior-lightweight bout and was taken to the Christian University Hospital in eastern Jakarta.
He underwent surgery on Wednesday, but did not survive the procedure.
Dr Tommy Halauwet confirmed Afrizal's death. He said: "The medical team from the UKI Hospital had tried to treat him, but his injury was really severe and we couldn't manage to save his life.
"Fight inspectors should have warned the referee to stop the fight since Afrizal had been repeatedly downed during the fight."