The speedy second baseman tested positive for the performance-enhancing substances exogenous testosterone and clostebol, MLB said. A league source told ESPN's Jayson Stark that Gordon tested positive during spring training.
In a statement Friday, Gordon said he did not knowingly take PEDs but was accepting the suspension.
"Though I did not do so knowingly, I have been informed that test results showed I ingested something that contained prohibited substances. The hardest part about this is feeling that I have let down my teammates, the organization and the fans," Gordon said. "I have been careful to avoid products that could contain something banned by MLB, and the 20-plus tests that I have taken and passed throughout my career prove this. I made a mistake, and I accept the consequences."
The league source told Stark that Gordon initially fought the suspension but dropped an appeal after Thursday's win over the Los Angeles Dodgers.
Gordon, 28, is in his sixth season in the majors. He will lose about $1.65 million in salary during the suspension and is ineligible for the postseason. Gordon signed a five-year, $50 million deal with Miami in January.
The suspension comes after Gordon won the NL batting title in 2015, when he hit .333 with 58 steals and 88 runs scored for the Marlins. He was given a diamond-filled pendant by Marlins owner Jeffrey Loria on April 19 to honor last season's batting title.
This is the first season of Barry Bonds' tenure as Marlins hitting coach. Bonds' legacy has been tainted by questions of PED use while he was a player.
The news was announced soon after the Marlins wrapped up a 5-3 road victory, which completed a four-game sweep of the Dodgers. Gordon had a key hit from the leadoff spot and went 1-for-4 with a run and an RBI.
Dodgers manager Dave Roberts said Friday that in the wake of Gordon's positive test, the team asked questions but found no avenue for protesting the results of the Marlins' four-game series sweep over the Dodgers.
Third baseman Martin Prado said the Marlins would continue to play at a high level.
"I really have nothing else to say," Prado said, according to the Miami Herald. "We had a great series, and we played good baseball, the whole team. We have to continue to do that. We have a game tomorrow, and we're going to play good baseball against a pretty good team, and we want to keep that streak going."
Marlins manager Don Mattingly managed Gordon during his first three big league seasons in Los Angeles before he was traded to Miami in a seven-player deal in December 2014. Mattingly took over as Marlins manager prior to this season.
"These guys love Dee, and we're going to support him," Mattingly said. "I feel like Dee's one of my kids, to be honest with you, because I've known him so long. So we're going to love him, and then we're going to support him. He's been a big part of the success that we've had."
Gordon, the son of former major league pitcher Tom Gordon, has made two All-Star teams and won the Gold Glove and Silver Slugger awards at second base last year. He is batting .266 with six stolen bases this season.
"Dee Gordon is a very important part of our team, and we all love him and support him," Marlins president David Samson said. "That said, I don't like or condone what he did. He is an important member of this organization and will be for many years to come. It's a huge, huge disappointment to the kids, to our fans, to his teammates and to everyone in our organization every single day.
"He will be back 80 games from now, and he will be welcomed back to this organization. But in the interim period, we expect him and we are positive that he will do everything that's necessary to make it up to his fans, to his teammates and to this organization."
"You shouldn't be allowed to [affect] games while appealing," Verlander said.
Harper said this situation is "definitely a disappointment," but the Nationals star, who finished second for the 2015 NL batting title, said he should not be considered the reigning batting champ because of Gordon's actions.
"I lost the batting title. I lost it completely," Harper said. "I was hitting like .345 with three weeks left or so. I completely lost it. It was nothing to do with that. You've still got to hit the baseball. You've still got to perform. And he did that. I completely lost the batting title last year, so that's all behind us."
Information from ESPN's Doug Padilla and Buster Olney and The Associated Press was used in this report.