The appeal was filed by the Major League Baseball Players Association on Wednesday. The union's executive director Michael Weiner said Rodriguez had the association's full support.
Rodriguez was suspended for 211 games - through to the end of the 2014 season - on Monday by MLB for a range of drug-related offences.
Rodriguez has denied any wrongdoing and immediately declared his intention to appeal.
MLB said the suspension would not kick in until Thursday, allowing the 38-year-old Rodriguez to play for the Yankees on Monday and Tuesday.
Now that he has appealed, Rodriguez is free to continue playing until his case is heard by arbitrator Fredric Horowitz.
Local media have said a ruling was not expected until November or December at the earliest, well after the season has finished.
Rodriguez was asked about his appeal by reporters before Wednesday against the White Sox in Chicago but said only: "I have no reaction to that."
Rodriguez was one of 13 players suspended by MLB on Monday in connection to the Biogenesis investigation.
The other 12 players were all offered 50-game bans which they accepted. Rodriguez was given a longer penalty because he was accused of other offences, including lying to the investigators.