CAS ruled there was insufficient evidence to show they had broken doping rules during the 2014 Sochi Winter Olympics.
But the IOC said Monday its invitation review panel examined applications on behalf of the 15 individuals and had lingering suspicions about potential anti-doping violations.
The row puts the IOC, which has always claimed to have the final say on which athletes compete in the Games, at loggerheads with sports law's highest court just days before the Olympics begin in South Korea on February 9.
IOC president Thomas Bach called the CAS decision "extremely disappointing and surprising."
"We would never have expected this," the 64-year-old German told a news conference in PyeongChang.
Bach added: "The privilege to be invited requires more than just the absence of a sanction."
The IOC will consider whether to appeal against the decision once it has seen the full details behind the ruling.
Bach also claimed the decision "shows the urgent need for reforms in the internal structure of CAS."
In December 2017, the IOC barred Russian athletes from competing in the 2018 Olympics over allegations of state-sponsored doping by Russia in Sochi.
However, Russian athletes who can prove they are clean will be invited to compete under a neutral flag
, and will be known as Olympic Athletes from Russia (OAR).
They will wear a uniform with that name on it, and the Olympic anthem will be played at any medal ceremonies for Russian athletes.
The IOC said in a statement the purpose of the review panel was "to confirm that athletes can be considered clean for a potential invitation to the Olympic Winter Games."
It said the panel took into account extra information about the athletes sent to it by the World Anti-Doping Agency (WADA) which had "raised suspicion about the integrity of these athletes."
At least 168 Russian athletes are participating in the Games, according to the PyeongChang official website. None of the athletes whose bans were overturned feature in the list.
In a further 11 cases, CAS ruled that doping violations had been committed but that lifetime bans were not justified and the punishments were reduced to a ban for the 2018 Games alone.
The IOC said at the time the CAS decision could have a "serious impact on the future fight against doping," and added that it could appeal against the decision at the Swiss Federal Tribunal, the country's highest court.
Meanwhile, in another blow to the anti-doping fight, The Sunday Times claims it has seen evidence that suggests widespread blood doping in endurance skiing events
between 2001 and 2010.
The paper, in conjunction with German broadcaster ARD, says hundreds of skiers, including some medalists, have escaped bans despite highly abnormal blood test figures.
WADA has contacted the media outlets for more information, the anti-doping body said in a statement.
"As always, WADA is committed to doing what's necessary to ensure a level playing field for clean athletes of the world and, as a result, we take these reports seriously," said WADA's director general Olivier Niggli.
Last month Russian President Vladimir Putin admitted there had been "instances of doping use
in Russia," but said the issue was a global problem.
Addressing supporters last Tuesday, Putin said: "There were instances of doping use, true -- I want the audience to know this and the whole country to know this," adding, "there are many such examples around the world, but no one is making a big show of it."