The International Amateur Boxing Association, or AIBA, overturned a decision that had been made on Wednesday, one in which Magomed Abdulhamidov of Azerbaijan was given a 22-17 bantamweight decision over Japan's Satoshi Shimizu.
Although Abdulhamidov led in points, he was also knocked down six times in the third round by his Japanese opponent.
The rules used for the Olympics state that if a boxer suffers three legitimate knockdowns, the fight is stopped.
Instead, referee Ishanguly Meretnyyazov let the bout go on. Shimizu was declared the winner Thursday, 24 hours after the bout, and the referee was expelled.
"I deeply regret that we had to take these decisions," said AIBA president Ching-Kuo Wu. "Our main concern has been and will always be the protection of the integrity and fair play of our competitions. I will take all possible steps to reinforce this."
The action in the ring Thursday continued to go poorly for the Americans, who won their first four bouts of the Olympics and have lost seven in a row since then.
The latest casualties were middleweight Terrell Gausha, who dropped a 16-15 decision to a boxer from India identified only as Vijender, and lightweight Jose Ramirez, who was defeated 15-11 by Fazliddin Gaibnazarov of Uzbekistan.
Cuba's Yasnier Toledo Lopez won his lightweight bout over Liu Qiang of China to reach the quarterfinals and will now meet Gani Zhalauov of Kazakhstan