Those weren't the only reasons they were upset.
New York manager Joe Girardi protested the game because of a mixup with the Marlins lineup in the eighth inning, when a Florida player was removed in a double switch but took his position on the field anyway.
"We've never seen it," Girardi said. "Something doesn't add up."
Sabathia came out in the second with tightness in his left biceps and the Marlins took advantage, handing New York its fourth loss in five games -- all against Washington and Florida. But Sabathia said he didn't want to be pulled because the injury wasn't serious. He expects to make his next start.
"It wasn't a sharp pain or anything," Sabathia said. "It just felt a little tight. It's something I felt before, between starts or something. It's nothing major."
Chris Volstad (5-7) gave up three runs in six innings. Matt Lindstrom allowed a two-run triple to Brett Gardner with two outs in the ninth, then got Derek Jeter to ground out for his 14th save in 16 chances.
Ramirez tied it with a two-run homer in the fifth, and Ross' solo shot off Brett Tomko (0-2) in the sixth put the Marlins ahead for good.
Rodriguez returned to the Yankees' lineup after being benched the past two games, ending his 0-for-16 skid with a two-run single in the third during his first start ever in his hometown of Miami.
But a Marlins move led to the protest.
In an odd mixup, Chris Coghlan started the top of the eighth in left field after Florida manager Fredi Gonzalez had removed him in a double switch. Alejandro De Aza batted for pitcher Renyel Pinto in the seventh and was supposed to take over in left, but never ran on the field.
Leo Nunez threw a pitch, then Girardi came out to protest. After about a 5-minute delay, Coghlan was removed, Jeremy Hermida went to left field and the Yankees played the rest of the game under protest. They were trailing 6-3 at the time.
Girardi thought Nunez should have been ruled out of the game as well once the mistake was recognized.
"But I'd like to keep the two runs I got in the ninth," Girardi joked.
Gonzalez agreed that a mistake was made but didn't think it changed the outcome.
"It was messed up. I'll take responsibility for it," Gonzalez said. "We lost both De Aza and Coghlan on it, but we got Hermida in there."
The protest will go to the commissioner's office for review.
There wasn't much for the throng of New York fans in attendance to cheer about in this one.
A team trainer went out to watch Sabathia while he warmed up before the second inning. He gave up a one-out double to Brett Carroll, then Girardi and a trainer came out to check on the left-hander again before taking him out of the game.
The 2007 AL Cy Young Award winner, Sabathia was the Yankees' biggest offseason pitching acquisition. He signed a $161 million, seven-year contract after spending 2008 with Cleveland and Milwaukee. Sabathia gave up one run and three hits in 1 1/3 innings.
He didn't get much of a pick-me-up.
Jorge Cantu hit an RBI single to left with two outs in the seventh and Melky Cabrera's wild throw home allowed another run to score, putting Florida ahead 6-3. Ramirez scored from first on the play, and Cantu went all the way to third on the error.
Greeted with a mix of cheers and boos, Rodriguez hit a two-run single in the third to give New York a 3-1 lead after Mark Teixeira hit an RBI double earlier in the inning.
Rodriguez said he reserved about 100 tickets for family and friends, including his mother and high school coach, but he didn't give them much else to cheer about. He finished 1 for 4 with two strikeouts, including one leading off the ninth.
The three-time MVP had been benched the past two games for what he and the team called fatigue, and Girardi said he will try to rest Rodriguez one day per week until the All-Star break to avoid him tiring in the future.
Rodriguez missed the start of the season following hip surgery and had played in every game since rejoining the Yankees on May 8. All that followed a wild offseason that included his admission that he used steroids from 2001-03 with Texas.
"I'd been looking forward to this day for a long time," Rodriguez said. "I wish we could have had a different outcome."
New York LF Johnny Damon, who made a crucial error in Saturday night's loss, did not start because of a sore right calf. He is not expected to miss more time. Cabrera moved over to left, with Gardner starting in center. ... Former broadcaster Roy Firestone sang the national anthem.