Kosovo and Gibraltar became the 210th and 211th members of the world football organization in votes taken at FIFA's annual congress in Mexico City.
The Serbian football federation's vice president vowed to legally challenge the decision even before the congress voted 141-23 to admit Kosovo.
"I sincerely and warmly thank you for this decision," Kosovo football federation president Fadil Vokrri told the congress. "In a region still ravaged by the horrors of history, football will give a better life to communities of Kosovo."
Normally, a player with dual nationality who has played for one national team cannot switch back to his second country. FIFA says that in the case of Kosovo, it will look at individuals on a case-by-case basis.
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Kosovo unilaterally declared independence in 2008, a decade after the 1998-1999 war between ethnic Albanian guerrillas and Serbian forces. More than 100 countries recognized its independence, but it is not a United Nations member and Belgrade refuses to accept the separation.
As for Gibraltar, FIFA's executive body originally rejected its bid, but the Court of Arbitration for Sport (CAS) ordered that the congress take a vote on the British territory, which is also claimed by Spain.
An overwhelming majority of FIFA members, 93 percent, voted to admit Gibraltar, which has a population of just 32,000 people.
Spain ceded Gibraltar to Britain in 1713 but has long argued that it should be returned to Spanish sovereignty. London says it will not do so against the wishes of Gibraltarians, who are staunchly pro-British.
"As a small country we are realistic about what we can achieve on the pitch but that is not the point... The point is that our many children who love our sport and who now will be the first generation of Gibraltarians to grow up with FIFA membership... They will be able to dream.