Penn met Guzman in a jungle in central Mexico in October for the interview, several months after the head of the Sinaloa drug cartel escaped from a high-security Mexican prison in July.
Guzman was recaptured on Friday and returned to prison. Penn's interview with Guzman was published online the next day. The Hollywood star called it "the first interview El Chapo had ever granted outside an interrogation room."
Sources in Mexico said the interview helped Mexico's government catch the world's most-wanted drug lord.
Long considered the bible for rock music lovers, Rolling Stone is also known for edgy journalism typified by correspondents like Matt Taibbi, who skewered Wall Street titans during the global financial crisis, and Hunter S Thompson, originator of the gonzo style of journalism.
Rolling Stone faces lawsuits over the article detailing a fraternity rape at the University of Virginia. A police investigation later found no evidence the alleged victim had been gang-raped.
A review by the Columbia University journalism school, commissioned by Rolling Stone and released last year, cited the magazine for reporting and editing lapses. Rolling Stone apologized for "discrepancies" in the account after the story sparked a national debate over sexual violence on college campuses.
In the interview with "El Chapo," Penn agreed to conditions set by Guzman, including allowing him to review the article before publication and changing the names of some sources and places to protect their identities.
A Rolling Stone spokeswoman said publisher Jann Wenner was not available for comment on Sunday.
Andrew Seaman, chairman of the ethics committee of the Society of Professional Journalists, criticized allowing a source to review and approve an article before publication.
"Allowing any source control over a story's content is inexcusable. The practice of pre-approval discredits the entire story - whether the subject requests changes or not," Seaman wrote in a blog post on Saturday night.
But Vice News reporter Danny Gold tweeted late on Saturday: "Never a fan of Penn's journalism but me and every other journo would have compromised a whole lot more to get an interview with El Chapo."
Marty Baron, executive editor of the Washington Post, tweeted a link on Sunday to an article headlined "Censor or die" about the intimidation techniques that cartel members apply to Mexican journalists to pressure them to censor the news.
"Good moment to remember what happens to real journalists who cover Mexican drug traffickers," Baron said.