Tampa Bay outfielder Jonny Gomes was also suspended two games for his involvement. All three players were fined, along with Yankees manager Joe Girardi and coaches Kevin Long and Bobby Meacham.
The announcement was made on Friday by Bob Watson, Major League Baseball's vice president of on-field operations. The suspensions, unless appealed, would begin at the start of the regular season.
"Obviously, it will hurt if you're missing two guys for three games," Girardi said. "You have to deal with it."
The incident took place in the second inning of Wednesday's game at Progress Energy Park in St. Petersburg, where Duncan slid hard into second base, spiking Rays second baseman Akinori Iwamura.
Saying that he has not had time to digest the ruling, Duncan commented that he initially felt the suspensions were "unfair."
"I spent six years in the Minor Leagues scratching and clawing to get where I am today," Duncan said. "I've worked as hard as I can every single day and left my heart and soul out on the baseball field every single game.
"I've been completely drained when I go in the clubhouse. I never let a single player or team out-hustle me on the field. I take pride in my work ethic and how I play this game. I'll continue to play as hard as I can."
Watson said that Duncan committed "violent and reckless actions, which incited the bench-clearing incident," and Cabrera made "violent and aggressive actions during the incident." Gomes was suspended for "violent actions, which escalated" the situation, charging in from right field and hitting Duncan from behind after the play was completed.
A video review of the incident showed Cabrera punching Rays third baseman Evan Longoria during the incident at second base. Longoria said on Wednesday that one Yankees player hit him in the back of the head, which was revealed to be Cabrera.
"[Cabrera's] name wasn't something that popped into this thing until today," Yankees general manager Brian Cashman said. "That's not something I was expecting."
The Yankees will open the regular season at home against the Blue Jays on March 31, while the Rays will open against the Orioles in Baltimore on the same date. Cashman said that he did not know if either player planned to appeal; Duncan said he had not decided.
The two clubs sparked a Spring Training rivalry last Saturday in Tampa when Rays infielder Elliot Johnson hit Yankees catcher Francisco Cervelli in an aggressive ninth-inning collision, fracturing the backstop's right wrist and requiring two screws to be surgically installed. Girardi immediately criticized the play as "unnecessary."
The next day, Duncan spoke to reporters and delivered comments that some believed -- Gomes included -- proved premeditation on Duncan's part to seek revenge on the Rays.
"For some reason, people assumed I made retaliatory remarks, which I never did," Duncan said. "Not one time did I ever make a comment about retaliation, or foul play or about playing this game dirty or malicious.
"Someone asked how I was going to play the game. I told everyone who asked me, 'I was going to play the game hard. I was going to match their intensity, or even exceed it.'"
The Rays and Yankees will meet twice more in Grapefruit League play, including a split-squad matchup at Legends Field on Saturday. Girardi said that Duncan will be listed on New York's roster for that game.
Even though Tampa Bay manager Joe Maddon removed Gomes from the travel roster just to avoid a third incident, Yankees shortstop Derek Jeter said he did not expect a third chapter would unfold on Saturday.
"Why would it linger on? Why would you continue to do it?" Jeter said. "If something happened, it would be stupid. It gets to a point where it's got to end."
Duncan has repeatedly said that he will not back off his aggressive style of play.
"If you truly in your heart believe that there's a right way to go about stuff, you should be true to yourself," Duncan said. "I'll continue to play the game with the same intensity."
Jeter, the Yankees' captain, said that Duncan's style fits his team.
"Shelley plays hard all the time," Jeter said. "He breaks up two, he runs hard all the time and that's just the type of player he is. That's why he's got the opportunity he's got. If I was Shelley, I wouldn't change the way I play the game. There's no reason to change the way he plays the game."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.