All athletes and officials from the four West African nations affected by the deadly virus will be "subject to regular temperature and physical assessment" for the duration of the games, which open Saturday in the eastern city of Nanjing.
The International Olympic Committee and Chinese organizers issued a joint statement saying they had worked out a safety policy in conjunction with the World Health Organization to prevent the possible spread of the virus that has killed more than 1,000 people in Guinea, Sierra Leone, Liberia and Nigeria.
"We have been reassured by the health authorities that there have been no suspected cases and that the risk of infection is extremely unlikely," the statement said.
However, athletes from the affected region will be prohibited from competing in combat sports due to "health authority guidelines" and aquatic events "based on the inability to completely exclude the risk of potential infection," the statement said.
The measures mean that three African athletes — two in combat sports and one in aquatics — won't be able to compete. The statement did not identify the athletes or countries involved.
However, according to the competitors' list on the official games website, a 16-year-old female Nigerian wrestler, and a 16-year-old female judo athlete and a 16-year-old male swimmer from Guinea won't compete.
The three who aren't allowed to compete will be invited back to Nanjing later to take part in another sporting competition, the IOC statement said.
"We regret that due to this issue some young athletes may have suffered twice, both from the anguish caused by the outbreak in their home countries and by not being able to compete in the Youth Olympic Games," it said.
The 12-day Youth Olympics are expected to attract more than 3,000 athletes from around the world, from the ages of 15 to 18, competing in 28 sports.
Organizers maintained that the delegations from the four Ebola-affected nations were still "welcome" at the games, after Sierra Leone said its team was told not to come to China at all and Nigeria reportedly complained that its athletes were being "isolated" and "quarantined" and not allowed to train alongside other competitors.
"Together we have developed a policy which balances the health needs of all, with respect for the rights of the young athletes from the region," the statement said. "The organizing committee has made it clear that all delegations are welcome to the games and each country is free to take their own decision on attendance."
Teams which are unable to come can still have their national flag carried into the opening ceremony and raised at the sports venues, the statement said.
The IOC told The Associated Press earlier Friday that no athletes from Sierra Leone and Liberia would be competing at the games after teams from those countries decided not to travel to China. Guinea will be represented.
The position of Nigeria was unclear, however, after the latest country to be affected by Ebola reportedly withdrew its athletes over their treatment in China.
"Nigerian athletes were quarantined, isolated and barred from training alongside athletes from other countries since they arrived," Gbenga Elegbeleye, the director general of Nigeria's Sports Commission, was quoted by Nigerian media as saying. "Following this discrimination, we have resolved to pull out from the games."
The Nigerian Sports Commission didn't immediately respond to requests from the AP for comment.
Sierra Leone's Olympic committee said this week that it had been advised by the Chinese embassy in Sierra Leone not to send a delegation to the games. The team had started its journey to China, the national Olympic committee said, but decided to turn back and now wouldn't compete at all.
The Ebola outbreak in West Africa has forced qualifiers for football's African Cup of Nations to be moved out of Guinea and Sierra Leone.