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.
That's easy to say thousands of kilometers removed from the atrocities. There's a high likelihood that someone from her family or friends was killed, raped, or deported by someone from that other athelete's friends or family. Whether or not you agree with the IOC ruling, show some fucking compassion for the athlete.
Furthermore let's not ignore the fact that the Olympics have ALWAYS been politicized, and these things fucking matter. There are entire paragraphs on Jesse Owen's wikipedia speculating on whether or not he shook Hitler's hand, because Hitler snubbed the medal presentations because he was pissed that "coloured people" were winning.
Even taking a completely cynical look at things, the optics are extremely important, and all of this, from both atheltes' behavior to the IOC's reactions, are ALL political statements to a degree or another, and everyone imvolved is a grown-ass adults who didn't have to hide behind a rulebook if they didn't want to.