Following the Italian Grand Prix in which Perez finished second to team-mate Max Verstappen, Marko suggested the Mexican driver's inconsistent form was due to his ethnicity.
Marko told Red Bull's own Servus TV channel: "We know that he has problems in qualifying, he has fluctuations in form. He is South American [sic] and he is just not as completely focused in his head as Max [Verstappen] is or as Sebastian [Vettel]."
Aside from the factual error, with Perez heralding from North America, Marko's comments have drawn widespread criticism for making a racial stereotype.
In response, the FIA has confirmed to Motorsport.com that Marko has been issued with a written warning.
A statement from the governing body read: "We can confirm that Helmut Marko has received a written warning and been reminded of his responsibilities as a public figure in motorsport in line with the FIA Code of Ethics."
Marko released his own public apology and had a private call with Perez.
Red Bull team boss Christian Horner told Sky Sports that the team had not issued a statement addressing the matter since Marko is "not an employee of Red Bull Racing."
He said: "Firstly those comments were, they weren't right. Helmut quickly recognised that and apologised for that both publicly and directly to Sergio.
"He spoke directly to Sergio about it and I think you're always learning in life, even at 80 years of age, and inevitably lessons have been learned.
"He's not an employee of Red Bull Racing so in terms of why didn't we put out a statement, he's part of the Red Bull wider group and the Group issued that apology through the Servus TV channel.
"We've spoken about it, I know he regrets what he said."
Perez says he took no offence from the comments owing to a strong personal relationship with Marko.
"I didn't get offended at all personally. Let's say if those comments were from a different perspective or so on, I would have to take them differently.
"But to me, it's just how things are, and I didn't take them personally."
He added: "I think we all make mistakes… What happens afterwards, and on the media side or in public, that's not in my control."
Marko has also drawn criticism from F1 team principals.
Mercedes motorsport chief Toto Wolff said: "We're laughing about South America. But it's a topic that's not at all funny. It's not only what has been said, but it's the mindset, that you can even come up with these things. That hasn't got any place in F1.
"That's not something that should have been said in the past, and certainly not now, and in the future.
"We all know that we need more diversity in F1, more inclusion, and the teams do their best to create an environment where this is possible.
"Obviously, statements like this don't shine the light on F1 that F1 deserves for all of the activities."