Outfielder Justin Ruggiano was recalled from Triple-A Durham to take Pena's place on the roster.
"I'm extremely heartbroken, because I want to be out there playing," Pena said. "It is what it is, but at this moment, I'm just going to go through the process to get better."
The injury occurred in the first inning of Tuesday night's game, when Pena got hit by a pitch from Justin Masterson. Despite getting hit, Pena went on to hit a double and a home run, teasing the Rays that he was about to get on a roll.
"We're going to wait two weeks and reevaluate it," Rays manager Joe Maddon said. "It's tough. He swung the bat well [Tuesday]. He had shown that back and forth, back and forth, and I knew it was only a matter of time before he got hot. It's just unfortunate. He really wanted to try and go through this thing. But talking to the doctors, it seems like the prudent thing is to reevaluate in two weeks and then create the plan after that. And that's what we're going to do."
Pena said he wanted to try to play through the injury until doctors pointed out that the crack in his finger could worsen, which might lead to surgery requiring a screw and a plate to be inserted.
The finger "seemed like it was going to be all right," Pena said. "But this morning it was extremely swollen, so we went to check it out and there is a fracture in there. Now it's a matter of getting better and getting back out there."
Pena, who was the team's MVP last season and the 2007 American League Comeback Player of the Year, has had a tepid beginning this season with a .227 average, 11 home runs and 35 RBIs. But his loss will be another in a series of losses the team has suffered recently. Closer Troy Percival went on the DL last week and Carl Crawford's right knee is dinged up, which kept him out of the starting lineup for Tuesday night's game.
"It's a pretty good test right now," Maddon said. "It's equivalent to the SATs in some respects right now. You have to play through these kinds of things to be good. And we have very worthy replacements. The lineup we're putting out there tonight is a pretty good lineup, also. Of course you never want to lose Carlos and you never want to lose Percy or Carl, but it happens. In the course of a championship season, it happens. And we just have to deal with it and move on, like everybody else does."
Pena believes the team will handle his absence well.
"We understand we have to overcome adversity to become a championship team," Pena said. "We have all the necessary tools, including the most important one, which is character. This is a team, not a one-player scene here. My absence should have no effect on how we go."
Ruggiano, 26, who begins his third stint with the club this season, has been doing well at Durham, where he was hitting .325 with five home runs, 27 RBIs and 12 stolen bases in 33 games.
Maddon said Ruggiano will give the club an added right-handed bat against left-handed starters and he will help back up Crawford in left. He added that Ruggiano will start Thursday night against Red Sox lefty Jon Lester.
Bill Chastain is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.