The match, which the US won 2-0, was delayed for close to five minutes in the 88th minute and again briefly in the 96th minute due to homophobic chants.
"Security staff in the stadium identified and ejected a significant number of fans, and the referee and match officials activated the FIFA protocol," the governing body said in a statement.
"It is extremely disappointing that this matter continues to be an issue at some matches, particularly in the context of the next two years presenting such a tremendous opportunity to grow the sport in our region.
"We will continue to urge fans to support their teams positively and with respect for the opposition and all participants in the game."
US manager Gregg Berhalter and players were hit by objects thrown onto the pitch while celebrating Gio Reyna's 63rd-minute goal.
"That was unfortunate because we want a really competitive game, we want a great atmosphere but we don't want to get things thrown at us," Berhalter told reporters. "It's unsafe and someone can get hurt."
Last year's Nations League semi-final between the US and Mexico in Las Vegas was also stopped due to discriminatory chants by spectators.
World soccer's governing body FIFA sanctioned the Mexican Football Federation (FMF) 100,000 Swiss francs ($111,000) for offensive chants made by Mexican fans at two games in the 2022 World Cup in Qatar.
