Despite placing first, Valieva's score was eight marks below what she was awarded when she performed the same routine at the Olympic team event.
She had looked determined as she began her performance, but her skate was not quite as polished as last week and at the end, she broke into tears, breathing heavily.
She collected herself to skate off the ice, but was still visibly distressed.
The teenager did not stop to speak to journalists, but walked straight past them flanked by members of her team, clutching her fluffy tissue box and sobbing.
Valieva had been favorite for gold going into the Olympics, but a week into the Games it emerged she had tested positive in December for trimetazidine, a drug usually used to treat angina but which also boosts endurance.
The Court of Arbitration for Sport ruled on Monday that she could carry on competing in the Chinese capital, although that does not mean that the Russian has been cleared of doping and could still face punishment at a later date.