Pineda experienced soreness in the back of his right shoulder during the Yankees' 13-9 win over the Philadelphia Phillies on Friday night.
"My arm is a little sore," Pineda said.
Pineda, bidding for a starting spot, allowed six runs and seven hits in 2 2/3 innings. The hard-throwing right-hander struggled with his fastball velocity again, averaging around 91 mph.
New York manager Joe Girardi said Pineda's injury likely has ended the competition.
"We're going to be careful with him," Girardi said.
Pineda also said he had issues with his mechanics, opening up his left shoulder while making pitches. He finished with two strikeouts and three walks, throwing just 40 of 71 pitches for strikes.
"I don't have that good command for my fastball," Pineda said.
Yankees general manager Brian Cashman said he is concerned about Pineda, who will have an MRI on Saturday.
"Hopefully we'll have some good news (Saturday)," Girardi said.
Pineda had not reported any problems before Friday night, according to Cashman.
Pineda was acquired from Seattle for slugging prospect Jesus Montero as part of a four-player trade in January. The 23-year old made the AL All-Star team last year in his rookie season, but was winless over his final seven starts.
New York left-hander Cesar Cabral also left with what Cashman called a painful elbow injury. The reliever will have X-rays and an MRI exam Saturday
"This has been a real bad day," Cashman said.
Carlos Ruiz had a three-run double during a four-run third against Pineda.
Curtis Granderson hit a two-run homer later in the third off Jonathan Papelbon, who was charged with four runs and three hits in two-thirds of an inning. He had given up just one run over his previous 10 innings.
Jim Thome doubled in three at-bats as the Phillies' designated hitter. With Ryan Howard set to begin the 2012 season on the disabled list while recovering from left Achilles' surgery, manager Charlie Manuel said Thome could start the season playing first base two or three times a week.
"He's looked pretty good," Manuel said. "If we can get two games a week out of him that would be fine, but sometimes if we can get three that would be even better."
Jimmy Rollins hit third Friday, which is something Manuel said could happen during the regular season.
"Jimmy can hit in the three-hole, he can hit anywhere," Manuel said. "We could have a different lineup a lot. I'm not saying every day, but we're going to have some lineups. We're in this to win, go ask ownership. We need to put the best lineup on the field we possibly can."
Hughes has been considered a frontrunner to be in the rotation, and appeared in line for a regular season start after his next outing was moved from Saturday to Sunday.
Garcia had another solid performance Friday, giving up one run and two hits over 6 2/3 innings in a Triple-A game.
"For me, this spring, I've pitched good enough so I'm happy," Garcia said.
Nova, a 16-game winner last season, will start Tuesday's road game in Port St. Lucie against the New York Mets.
Yankees right fielder Nick Swisher, out with a groin injury, played five innings of defense in the Triple-A game and should return Sunday.
"I'm, at least, almost ready to really take off the chains and just let it go," Swisher said. "I didn't feel it at all. Overall, I feel great as of right now."
Dewayne Wise homered twice and had three RBIs for the Yankees.
Philadelphia traded INF/OF Matt Rizzotti to Minnesota for cash considerations. ... Yankees RHP David Robertson allowed two runs and five hits over two innings in a Double-A game. Robertson, slowed earlier this spring by a bruised right foot, said he will be ready for opening day. "I think he's still developing arm strength," Girardi said. "I don't think he's far away." ... New York LHP Andy Pettitte is scheduled to throw his second simulated game Saturday and might pitch in Wednesday's home game with the Mets. ... DH/OF Jack Cust has been added to the Yankees' Triple-A Scranton/Wilkes-Barre roster. C Craig Tatum was outrighted to the International League club.