The Ecuadoran football federation said on Tuesday that defender Byron Castillo had been left out of the nation's World Cup squad to avoid further "unfair sanctions" in a dispute over the player's nationality.
Last week the Court of Arbitration for Sport ruled that Castillo was eligible to play in Qatar but sanctioned the federation over the "falsification" of his passport.
That cleared the way for the South American nation to take part in the World Cup after Chile and Peru had contested Ecuador's qualification over the eligibility of Castillo.
The Chilean football federation (FFCH) said there was evidence that the player was born in Colombia in 1995 and not in Playas, Ecuador, in 1998.
The FFCH alleged "use of a falsified birth certificate, false declaration of age and false nationality".
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World governing body Fifa ruled in September that Castillo, who played in eight of Ecuador's qualifiers, was considered to have "permanent Ecuadoran nationality".
The case went to the CAS, which partially upheld the appeals by Chile and Peru.
The court said Castillo was eligible to play for Ecuador in the qualifiers "considering that the Ecuadoran authorities acknowledged Byron Castillo as an Ecuadoran national".
But it added: "While the player's Ecuadoran passport was indeed authentic, some information provided therein was false.
"In particular, the panel was comfortably satisfied that the player's date and place of birth were incorrect since the player was actually born in Tumaco, Colombia, on 25 June 1995."
The football federation was ordered to pay a fine of 100 000 Swiss francs, and the men's team will be docked three points in the 2026 World Cup qualifiers.
The FEF described the CAS ruling as "arbitrary" and "without legal basis."
The federation said in a statement on Tuesday that Castillo would not be travelling to Qatar.
"Faced with the risk of more unfair sanctions, the Ecuadoran Football Federation is obliged not to include the player Byron Castillo Segura in the final list presented to Fifa," it said.
Castillo on Tuesday uploaded a photo of the Ecuadoran team to his Instagram account, wishing them well and stating: "My dream doesn’t end here, I stand firm."
Ecuador feature in the first match of the World Cup, against host nation Qatar, on Sunday.