The pause occurred the final moments of the second half before it into extra-time.
Play resumed after three minutes as players on both sides pleaded to the crowd to use the chant.
It is the second time a match has been halted at the tournament at Denver’s Empower Field at Mile High, when Mexico’s semifinal win over Costa Rica was also briefly paused.
That match also saw several fans ejected from the stadium.
Mexico have struggled throughout the years with stopping supporters from making anti-gay chants. In March, FIFA opened an investigation into anti-gay chanting from Mexico supporters during an Olympic qualifier against the Dominican Republic.