Guzman was captured on Friday in the city of Los Mochis in his home state of Sinaloa. Five suspected Sinoloa Cartel members were killed and one Mexican marine was wounded during the capture operation.
On Sunday, Rubio condemned Penn's seven-hour Rolling Stone interview with the former fugitive drug kingpin.
"If one of these American actors who have benefited from the greatness of this country, who have made money from our free enterprise system, want to go fawn all over a criminal and a drug trafficker in their interviews, they have a constitutional right to do it," Rubio said in an appearance on ABC's "This Week.". "I find it grotesque."
In the "El Chapo Speaks" article, Guzman boasted about his drug business, saying he "supplies more heroin, methamphetamine, cocaine and marijuana than anybody else in the world."
Rubio said he hopes Guzman is extradited to the United States, adding he was positive the interview helped lead authorities to Guzman.
"Sean Penn is not someone I spend a lot of time thinking about. I didn't even know he was still around," Rubio said. "I guess [the Mexicans] used the interview that he had in order to find him. That's fantastic. I hope they extradite 'El Chapo' to the United States."
Although Penn, with the help of Mexican actress Kate del Castillo, landed one of the most high-profile interviews in recent history, what Guzman did not know was that his attempts to reach out to the world would partly lead to his capture.
Attorney General Arely Gomez on Friday said an important aspect of his recapture "was discovering Guzman's intention to have a biographic film made," as he "contacted actresses and producers, which was part of one line of investigation."
No other details have been revealed on the process that led authorities to Guzman. Penn's interview is not directly named as the origin of the "one line of investigation" that led to Guzman's capture.