UEFA's Control, Ethics and Disciplinary Body rejected arguments presented by Portugal and Luxembourg's national federations, whose teams faced Ukraine in the first two rounds of Group B qualifiers for Euro 2020.
Morais, 32, who was born in Brazil, made his debut for Ukraine on 22 March against Portugal, the current European champions, coming on as a substitute in the 76th minute. The match ended nil-nil.
Three days later he was called up to play against Luxembourg, in a match that Ukraine won 2-1.
At issue is the allgeation that the player had not been living for a minimum of five uninterrupted years in Ukraine, as required under the regulations of FIFA, football's world governing body.
Moraes arrived in Ukraine in 2012 to play for Metalurg Donetsk. In 2016, having in the meantime trasferred to Dynamo Kiev, he left for China, before returning to play in Ukraine's national league in August 2017.
On that basis, both Portugal and Luxembourg questioned his eligibility to play for Ukraine.
FIFA statutes and regulations determine that to be eligible for a new nationality a player must meet one of four requirements, with the issue here whether Moraes had "lived continuously for at least five years after reaching the age of 18 on the territory of the relevant association."