Mariia Pomazan claimed gold on Friday in the F35/36 discus before organisers realised they had made a mistake due to a scoring error and promoted China's Wu Qing from second.
On Sunday the Ukrainian was told she could keep the medal but it would not count towards her country's medal tally.
"We have tried our hardest since Friday to find a solution with both the Chinese and the Ukrainians," International Paralympic Committee director of communications Craig Spence said on Monday.
"There has been a lot of negotiation but we've struggled and failed to reach a conclusion that suits all parties. Therefore, we have to go with the rule book, and so today the Chinese athlete will take the gold medal and the Ukrainian the silver medal."
The medals were originally to be handed out on Friday, but the ceremony was pushed back to Saturday, then Sunday and then Monday. Pomazan, demoted to silver, did not turn up to the rearranged ceremony at the Olympic Stadium.
"All combined-class field events use a points scoring system where final positions are determined by points rather than distance," Paralympic organisers said in a statement on Sunday.
"In the women's combined-class discus event, incorrect medals were awarded following the use of inaccurate results data. We sincerely apologise to the athletes affected.
"The inaccurate data also affected the men's shot put F42/44, although the final medal placing was not impacted."
In total, seven out of the 10 positions had to be changed.
Pomazan put the fiasco behind her to win gold in the women's shot put on Sunday.