The decision by UEFA's appeals committee came 10 days after Metalist lost an appeal at the Court of Arbitration for Sport (CAS).
Metalist, runners-up in last season's Ukrainian Premier League, have already knocked Greek side PAOK out of the competition and were due to visit Schalke on August 21 with the return on August 27.
UEFA said it's emergency panel would meet later on Wednesday to "consider the consequences of the decision on the competition."
Metalist said they would appeal to CAS and a ruling in their favour, which may not come until after the group stage has started, could throw the Champions League into confusion.
"We regret that such a sanction was applied, and we do not agree with it, that's why today we plan to appeal to the Court of Arbitration for Sport in Lausanne," Metalist first vice president Kostyantyn Pyvovarov said in a statement.
"Also, we have appealed to the Supreme Court of Switzerland with the application for suspension of CAS decision.
"I want to remind you that the match, which allegedly took place, was held back in 2008, with the old owners of the club. At the same time, Metalist has won the right to participate in the Champions League 2013/14 in a fair fight.
"Our team, our fans deserve to take part in the main football competition in Europe. I want to assure fans that we will fight for the rights of the club and protect them in accordance with all legal requirements."
Metalist were not the only club whose Champions League participation was shrouded in uncertainty.
CAS has already allowed Fenerbahce back into the competition while it considers an appeal from the Turkish club against their two-year ban from European competition over a domestic match-fixing case.
CAS have said they will make a final ruling on Fenerbahce's case by August 28, the day after the Turks play the second leg of their playoff tie against Arsenal.
Fenerbahce have already eliminated Salzburg from the competition.
Earlier this month, CAS upheld a Ukraine Football Federation (FFU) decision to fine Metalist Kharkiv and FC Karpaty $25,000 (16,090 pounds) each over the manipulation of a match played in April 2008.
The tribunal also confirmed bans of between three and five years on six Metalist players, plus fines of $10,000 each.
Metalist director Yevhen Krasnikov was banned from any football-related activity for five years.
Two Karpaty officials were given suspended bans and ordered to pay "compulsory cash contributions" to the FFU while CAS upheld an appeal by a third official from the club.
CAS said in its ruling that the two clubs "were held liable for the behaviour of their football players or officials under the principle of strict liability."
(Reporting By Brian Homewood, additional reporting by Olzhas Auyezov, editing by Pritha Sarkar)
