Shin was physically escorted off the piste after her team argued against the award of a winning touch to Germany's Britta Heidemann in the epee semi-final.
Heidemann ran off screaming with joy after the initial awarding of the touch but was then called back to await the final decision of the judge.
The defending champion from Germany later went on to lose the final to Ukrainian Yana Shemyakina while Shin was beaten 15-11 by top seed Sun Yujie of China in the bronze-medal match.
After initial discussions resulted in Heidemann being awarded the final touch in the semi-final, a stunned Shin did not move.
The Korean did not leave the piste as this would have indicated she accepted the decision of the judge, Austrian Barbara Csar. By staying, Shin was exercising her rights under the rules.
An indelible image of Shin will linger in the memory, a 25-year old looking dejected as she sits on a dramatically spot-lit piste, pristine in her white uniform with a towel draped over her shoulder.
The Korean was also surrounded by 7,000 screaming spectators, many unsure what was happening.
Her coach, Shim Jaesung, lodged a written complaint that was ultimately rejected by the FIE (Federation International d'Escrime), fencing's governing body.
"I did everything I could," Shim told Reuters while standing outside the FIE's office at the ExCel Centre.
Executive members of the FIE board were meeting late into the night discussing the contents of a statement due for release on Tuesday.
"They said your fencer has to continue the match so I had to accept the decision," said Shim.
"Shin told me, 'I am okay', but I fear she is not okay," added the drained-looking coach who also sits on the FIE rules committee.
Germany's fencing delegation head, Manfred Kaspar, and Shim were seen having calm discussions while the officials deliberated.
"I completely agree with my colleague from Korea's decision to make a protest against a refereeing decision. We are not angry," said Kaspar.
While the tip of a fencing blade is widely considered the second fastest moving object in sport, behind a marksman's bullet, in the match between Shin and Heidemann there were at least three separate actions while a single second remained on the clock.
The row erupted when two double-touches were recorded with a second to go and Shin thought she had triumphed. But a single second was put back on the clock after some discussions.
Heidemann then unleashed a blistering surge forward, hitting Shin while also avoiding her blade.