The International Fencing Federation (FIE) also said it was reinstating Kharlan, allowing her to take part in the team competition at the world championships in Milan.
Emmanuel Katsiadakis, the Greek president of the FIE, said the decision had been taken "after consultation with the International Olympic Committee".
Kharlan, the first fencer to face a Russian or Belarusian since the former's invasion of Ukraine, won 15-7 against Russia's Anna Smirnova on Thursday.
The 32-year-old four-time Olympic medallist refused Smirnova's handshake afterwards, instead offering her sabre to tap blades, but FIE rules state that the two fencers must shake hands.
Smirnova staged a 45-minute protest and refused to leave the competition strip.
Kharlan was disqualified, claiming afterwards that Emmanuel Katsiadakis, the Greek president of the FIE, had even assured her that it was "possible" not to shake hands and offer a touch of her blade instead following her victory.
"I thought I had his word, to be safe, but apparently, no," Kharlan said.
In response to her disqualification, the International Olympic Committee called for Ukrainian athletes to be treated "sensitively".
Then on Friday, IOC President Thomas Bach, a former Olympic fencer himself, sent Kharlan a letter saying she would be guaranteed a place at next year's Olympics in Paris regardless of whether she gained the qualification points.
They had nuclear weapons. Under a treaty with Russia to respect their borders, Ukraine gave them up. Russia broke that treaty. Now Russia is mad they could very well lose their 2014 gains and wants to negotiate peace, but Ukraine says absolutely not while we're still making progress on the offensive campaign, and Ukraine is about to launch an offensive on Crimea. Why would they give up ground they've gained and ground they could wrestle back?