FIFA slapped the Mexicans with a CHF 10,000 (£7,619) fine for what it called "discriminatory and insulting chants" during their surprise 1-0 win over Germany on Sunday.
Mexicans have long shouted a slang word for a male sex worker at games, which gay rights groups argue is homophobic.
The Mexican Football Federation (FMF) was sanctioned 12 times for homophobic chanting during the World Cup qualifying campaign, receiving warnings for the first two offences and fines for 10 more.
Hernandez posted a message on Instagram on Wednesday asking fans to end the derogatory chant that is usually shouted during their opponents' goal kicks.
"To all Mexican fans in the stadiums, don't shout 'Puto'," Hernandez said. "Let's not risk another sanction."
Although the Mexican team has appealed before for an end to the chants – the players even released a video on the subject in 2016 – some supporters have not relented.
The chant was widely heard at Mexico games in the 2014 World Cup in Brazil, when FIFA took no action, but the governing body has since launched a clamp-down. Other Latin American teams, including Argentina and Chile, have also been fined.
FIFA is employing three specialist observers at each World Cup match to report discriminatory behaviour by spectators.
FIFA also said it was fining Serbia because of their fans display of a political message in Sunday's Group E opener against Costa Rica.
"The FIFA Disciplinary Committee has sanctioned the Serbian Football Association with a fine of CHF 10,000 for the display of an offensive and political banner by Serbian fans during the match played between Serbia and Costa Rica,” FIFA said.
(Reporting by Andrew Downie; Editing by Tony Lawrence)
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