The loss snapped the Rays' two-game winning streak, while earning the Yankees a split of the four-game series. The Rays fell to 9-10 on the season, and the Yankees moved to 11-8 to remain in first place in the American League East.
Maddon opted to let rookie left-hander C.J. Riefenhauser walk Ellsbury and pitch to the left-handed-hitting Anna.
The decision "depended on who the pitcher was," Maddon said. "If it was somebody else [besides Riefenhauser], I may have not done that. But I had that much faith in Riefenhauser."
Riefenshauser, who made his Major League debut on Saturday night and retired the four hitters he faced, felt comfortable with the situation.
"I was kind of confident because I saw a lefty on deck, too," Riefenhauser said. "So I was like, 'Alright, let's do it.'"
Anna managed to hold back on a 3-2 Riefenhauser offering to draw the walk and plate Brett Gardner.
Maddon thought Anna swung, which would have ended the inning.
"There are so many different interpretations of the check swing -- and from my perspective, his hands were so far in front of home plate," Maddon said. "I know there are umpires when they see that, they're going to call it a strike. Tonight, they didn't call that a strike."
Riefenhauser allowed that he didn't know if Anna swung.
"It was close," Riefenhauser said. "I guess not, though."
Though the decision didn't go the Rays' way, Maddon stood by the rookie, who was optioned to Triple-A Durham after the game.
"Quite frankly, I would [make the same decision] -- believing that he would get this guy out," Maddon said. "That was just one of those moments where it didn't happen."
Added Riefenhauser: "It was a battle. I'm going to face him again, hopefully soon, hopefully a different outcome."
Josh Lueke replaced Riefenhauser, and he surrendered a two-run single to Carlos Beltran and an RBI single to Alfonso Soriano to push the Yankees' lead to 5-1.
Most perplexing to the Rays was the team's offense. After scoring 27 runs in their previous two games, the Rays scored just once on Sunday.
"This game is funny, and you go through stretches like that," Wil Myers observed.
And the problem wasn't the Yankees' pitching, according to Maddon, who wasn't exactly dishing out superlatives about the pitchers wearing pinstripes.
"I don't know [what happened]," Maddon said. "We've been swinging the bats so well. ... There's really no solid explanation. I can't stand here and say that the Yankees pitched that great. We just did not have a good offensive day."
Yankees lefty Vidal Nuno held the Rays scoreless on three hits through five innings.
"He's not used to pitching five innings like that," Maddon said. "We should have been able to break through at some point.
"...You think you might have turned some offensive corner. ... We just didn't have that today."
The Rays trailed, 1-0, through six innings before tying the game in the seventh on pinch-hitter Matt Joyce's sacrifice fly off Adam Warren that scored James Loney.
Cesar Ramos started for the Rays and had a much better showing than he did in his previous start against the Reds, when he logged just two innings.
Ramos allowed an RBI double to Gardner in the fourth, which was all the Yankees got against the left-hander in five innings. Gardner's double was originally ruled an out before Yanks manager Joe Girardi sucessfully challenged the play to have it overturned.
The Rays had a chance to win the game in the ninth, when they had runners on first and second with two outs. But Shawn Kelley struck out Jose Molina looking to end the inning.
Girardi came away pleased to split the series.
"That's a big win, after winning the first game the way we did and then to really get beat up the next two days," Girardi said. "To be able to bounce back and leave here 2-2, we've got a day off tomorrow to try to get ready for the Red Sox. I thought it was important."
In the other clubhouse, Maddon expressed disappointment.
"They're really good," Maddon said. "We're really good. It's going to happen that way. ... When you have a chance to go to the 3-1 series and miss out on that attempt when you only give up one run in nine innings and 10 innings and 11 innings, you'd like to be able to win that game at home."