Pena scored on the play and gave the Rays a lead they would not relinquish in a 4-3 victory over the Pirates at PNC Park.
The victory, coupled with Boston's 3-2 loss at Houston, vaulted the Rays over the Red Sox into first place heading into their three-game series in St. Petersburg beginning on Monday night.
"Not everyone on this team would have tried that," Rays manager Joe Maddon said of Pena's play. "And that, to me, was a big play because of course it got the bad throw. That was a big moment."
Before that inning, it looked like the Rays would squander their 12th Interleague win of the year. They allowed the Pirates to come back twice in the game.
The first time came in the fourth, when center fielder B.J. Upton committed an error on second baseman Freddy Sanchez's double to left-center field. Sanchez wound up scoring on Jason Bay's sacrifice fly, tying the game at 1.
The second comeback came in the sixth with a runner on third. Rays backup catcher Shawn Riggans, making a Sunday start for Dioner Navarro, came out too far on center fielder Nate McLouth's swinging bunt, which allowed shortstop Jack Wilson to score from third -- as no Ray was covering home.
"I had my head up my butt for a minute there," Riggans said. "I didn't expect him to get off the mound as good as he did. Luckily, we got out of there with a victory [and] that run didn't come back to bite us."
Riggans was correct, partly because his one-out RBI single in the eighth gave Tampa Bay a 4-2 lead. Riggans also gave the Rays their first lead of the game in the fourth with a home run to center field.
Aybar, making his second start of the series for suspended second baseman Akinori Iwamura, also contributed with a sixth-inning home run to make it 2-1.
"My main thing is I want to get our pitcher the 'W,'" Riggans said. "I could care less about the hitting. Hits are going to come and go without getting a ton of reps."
From there, the Rays bullpen shut down the Pirates in the last two frames. Closer Troy Percival, who has been nursing a sore left hamstring, made his first appearance since Tuesday and picked up his 19th save in the process.
"I'm definitely rested," the 38-year-old closer said. "I figured I had to make the right adjustment to take a lot of stress off of my front leg. When my leg gets completely right, I think with the arm strength I have it'll just climb really fast because my arm feels as strong as it has all year."
Sunday's victory gave starter Andy Sonnanstine his ninth win of the year. The right-hander threw seven quality innings, surrendering only one earned run on five hits. His lengthy outing gave the Rays' bullpen some much-needed rest after a pitching six innings of relief in Saturday night's 13-inning loss.
"I felt good," Sonnanstine said. "I felt like I was there for the whole game except for a handful of spots I missed. Going in there with the mindset that I know I'm going to go as far as I can, sometimes that's tough with National League rules. I feel really good about what happened."
The win also gives Tampa Bay a 5-1 record in its recent six-game road trip, and a 49-32 record at the halfway point of the season.
"I'm not going to sit here and say I expected us to be at this particular place in the standings," Maddon said. "But we have played well. Again, we've played really good defense.
"It's kind of been spread out. It's been an anonymous first half. There's no one guy having a killer season. Furthermore, it makes it more appealing to me that we're at this juncture being at the place that we are, knowing someone is going to turn into a beast in the second half."