A letter sent to Kharlan signed by International Olympic Committee President Thomas Bach said she would be granted an additional quota place at the Olympics if she failed to qualify.
"Rest assured the IOC will continue to stand in full solidarity with the Ukrainian athletes and the Olympic community of Ukraine during these extremely difficult times," it added.
Kharlan, a four-time Olympic medallist and world champion, won her individual sabre bout 15-7 and then refused to shake hands with Russian Anna Smirnova - competing as a neutral - at the World Championships in Milan on Thursday.
In fencing's rules, shaking an opponent's hand is mandatory and failure to do so results in a 'black card'.
Ukraine's Youth and Sports minister Vadym Huttsait welcomed the IOC decision in a Facebook post.
"Despite all the hate that my team and I have endured over the past 24 hours, after working persistently for the benefit of Ukrainian athletes and not responding to this, we now have our first result," he said.
"Work is continuing to rescind the "black card" for Olha's future competitions and to prevent similar situations in other sports."
Ukraine's Fencing Federation (NFFU) also backed Kharlan.
Ukrainian athletes in other sports - including tennis players Elina Svitolina and Marta Kostyuk - have also refused to shake hands with Russian and Belarusian opponents following Russia's invasion of Ukraine, with Moscow using Belarus as a staging ground for what it calls a "special military operation".
The IOC said earlier on Friday that international federations should handle situations involving Ukrainian and neutral athletes with sensitivity.
RULES RELAXED
Kharlan represented Ukraine in the fencing tournament after the country's sports ministry relaxed its rules over national sports teams taking part in Olympic, non-Olympic and Paralympic events with competitors from Russia and Belarus.
"The decision taken by the Ukraine sports ministry will allow Ukrainian athletes to participate in international competitions and will enable them to qualify for the Olympic Games Paris 2024," the IOC told Reuters on Friday.
"We are glad that they will be given this opportunity, and at the same time, we are aware of the difficult inner conflicts they may have, given the aggression against their country.
"Therefore, we encourage International Federations to handle situations involving Ukrainian and Individual Neutral Athletes with the necessary degree of sensitivity.
"We continue to stand in full solidarity with the Ukrainian athletes and the Olympic community of Ukraine."
TEAM SABRE
The NFFU appealed against Kharlan's disqualification and the International Fencing Federation (FIE) decided later on Friday to allow the fencer to compete in the women’s team sabre team competition at the World Championships.
The FIE stressed that it was still fully behind its original penalty, which was "in accordance and compliance with its official rules and associated penalties", but it would now allow Kharlan to take part in the team competition.
"...after consultation with the International Olympic Committee, we believe this decision is made in keeping with the Olympic Spirit," Interim President Emmanuel Katsiadakis said.
"It also sends a message of sensitivity and understanding to our members and all sports federations, as the world faces tremendous challenges."
Kharlan said she appreciated the change of heart.
"The most important thing for an athlete is to be able to compete, for my family, my team, my country and all the people who support me. During these difficult few days, I appreciate all the support I’ve had from around the world."
Kharlan said earlier that she stood by her decision not to shake hands with Smirnova.
"Today is kind of better because (of) all the support that I have... Everything that was going on, I think is a huge message for the people," Kharlan told Reuters on Friday.
"Rules must be changed... for Ukrainians because you have to understand we still have war, and during this war... we just can't... do handshakes, and you have to change, and you have to have some respect for us.
"When I have a choice... where I shake hands I will never shake hands with her. I'm sorry but there is something bigger than Olympic Games or license or fencing and finally, I understood that, there is something more. The support for the Ukrainian people it's incredible."
