FIFA said Mexico also was ordered to forfeit three under-23 matches in which it used Zendejas.
The governing body did not announce the penalty until Thursday, a day after it was contacted by The Associated Press following the U.S. Soccer Federation selecting Zendejas for next week's games against Serbia and Colombia, the first for the United States since the World Cup.
"FIFA can confirm that it has imposed a fine of CHF 10,000 on the Mexican Football Association for breaches of article 5 of the Regulations Governing the Application (RGAS) of the FIFA Statutes following the fielding of the player Alejandro Zendejas," the governing body said in a statement.
"Besides the fine, all matches have been declared forfeited. Based on the applicable provisions of the RGAS, the player remains however eligible to play for the representative teams of the USA."
Under FIFA's statutes, because Zendejas played in an official competition for a U.S. youth national team, he would have had to apply to FIFA for a one-time switch in affiliation to be allowed to appear for a Mexican national team.
Among the forfeits, FIFA listed a match against Ecuador on Oct. 28, 2021, at Charlotte, North Carolina, that Mexico lost 3-2 (Zendejas entered for Uriel Antuna in the 66th minute); and a game against Guatemala last April 22 at Orlando, Florida, that ended in a 0-0 draw (Zendejas started and played until the 72nd minute).
All the forfeits become 3-0 defeats.
The change in the senior national team matches will have a small impact on Mexico's FIFA ranking.
Zendejas was in the youth academy of Major League Soccer's FC Dallas, which listed him as having been born in El Paso, Texas.
He made his MLS debut against Houston on May 1, 2015, and transferred to Mexico's Chivas in June 2016, then was lent to Zacatepec in June 2017.
Zendejas transferred to Necaxa in June 2020 and to Club America in January 2022.
Zendejas was among 24 players selected Wednesday by U.S. interim coach Anthony Hudson for matches against Serbia next Wednesday at Los Angeles and vs. Colombia Jan. 28 at Carson, California.
He is among 13 players on the roster who could make U.S. national team debuts.
In a separate ruling on Wednesday, the Mexican Federation (FMF) announced that FIFA had revoked a one-match supporters' ban handed out last week due to discriminatory chants by fans at the 2022 World Cup.
"After having requested FIFA for clarification and the scope of the sanction, said governing body confirmed that the Mexican national team will be able to play its next match with spectators, with the understanding that the FMF is in a 2-year observational period," read a statement from the FMF.
Fans will now be able to attend Mexico's home against Jamaica on March 26 in the CONCACAF Nations League.