Rodriguez was among 13 players disciplined for involvement with the now-closed Biogenesis wellness clinic, but his punishment was the most severe. He was the only one of the group to lodge an appeal.
The three-time American League Most Valuable Player hadn't played this season due to hip surgery and a strained quadricep, but was inserted into the New York Yankees lineup at third base for Monday's game in Chicago.
He was roundly by the White Sox fans in his first at-bat in the second inning before collecting a bloop single against Chisox starter Jose Quintana.
Rodriguez finished the contest 1-for-4.
Baseball Commissioner Bud Selig said in a statement Rodriguez' suspension would cover the post-season in both 2013 and '14. The lengthy sanction was due to Rodriguez's "use and possession of numerous forms of prohibited performance-enhancing substances, including testosterone and human growth hormone, over the course of multiple years."
Rodriguez said before the contest against he has appealed the sanction.
"I am disappointed with the penalty and intend to appeal and fight this through the process," he said in a statement. "I am eager to get back on the field and be with my teammates in Chicago tonight. I want to thank my family, friends and fans who have stood by my side through all this."
During a pre-game news conference, Rodriguez said the PED investigation has taken a toll on him, NBC Sports reported.
"The last seven months have been a nightmare," he said. "Probably the worst time of my life, for sure."
Asked why he appealed, the slugger said, "I'm fighting for my life, I have to defend myself. If I don't defend myself, no one else will."
The other 12 players were handed 50-game suspensions, MLB said. There are about 50 games left in the 2013 regular season.
The suspensions are part of a broad investigation by MLB into allegations of PED use with substances obtained through the Biogenesis of America clinic in Coral Gables, Fla.
"I am proud of the comprehensive nature of our efforts -- not only with regard to random testing, groundbreaking blood testing for human growth hormone and one of the most significant longitudinal profiling programs in the world, but also our investigative capabilities, which proved vital to the Biogenesis case," Selig's statement read.
"Upon learning that players were linked to the use of performance-enhancing drugs, we vigorously pursued evidence that linked those individuals to violations of our program. We conducted a thorough, aggressive investigation guided by facts so that we could justly enforce our rules."
About 20 MLB players were accused of getting PEDs from the clinic. Milwaukee outfielder Ryan Braun, the 2011 National League Most Valuable Player, agreed to a 65-game ban last month that ended his season.
Although the usual suspension for a first PED-related offense is 50 games, Braun reportedly accepted a deal that locked him out of the rest of the 2013 season because of evidence MLB obtained through the Biogenesis investigation against him.
The players who were given the 50-game suspensions are: Philadelphia pitcher Antonio Bastardo, San Diego shortstop Everth Cabrera, New York Yankees catcher Francisco Cervelli, Texas outfielder Nelson Cruz, San Diego pitcher Fautino De La Santos, Houston pitcher Sergio Escalona, New York Yankees outfielder Fernando Martinez, Seattle catcher Jesus Montero, free-agent pitcher Jordan Norberto, Detroit shortstop Jhonny Peralta, New York Mets outfielder Cesar Puello and New York Mets outfielder Jordany Valdespin.
Toronto outfielder Melky Cabrera, Oakland pitcher Bartolo Colon and San Diego catcher Yasmani Grandal have already served 50-game suspensions related to the Biogenesis case and won't be further disciplined, MLB said.