Ellsbury singled to center field with two outs, driving home Brian Roberts to tie the score at 5. Juan Carlos Oviedo threw to first, and first-base umpire Doug Eddings ruled safe, but Maddon left the dugout and asked for a review.
The umpiring crew, led by chief Brian O'Nora, took one minute and five seconds to overturn the call on the manager's challenge. The replay showed Loney's glove nipping Ellsbury's knee with the tag.
"That was primarily done by Loney," Maddon said. "Loney gave me the head's-up fast that he thought he was out at first base."
The Yankees successfully challenged a call at first base in the 13th inning, resulting in a double play and indirectly prompting Maddon's ejection.
Facing Adam Warren with the score still tied at 5, Tampa Bay's Matt Joyce grounded into a forceout that was fielded by third baseman Yangervis Solarte, with pinch-runner Brandon Guyer being called out at second.
Solarte tagged the base and fired to first, where Joyce was ruled safe by Eddings.
After a review of one minute and one second, the on-field call was overturned and Joyce was called out for the second out of the inning. Maddon came out of the dugout to argue, believing that the replay had been inconclusive, and was ejected by O'Nora.
"I saw the replay, so I went out there," Maddon said. "I didn't think there was anything conclusive based on what I saw to overturn the call. My mind's eye, if there's nothing persuasive to reverse the call, then it should go back to the call on the field."
In the top of the 14th, Yankees manager Joe Girardi asked the umpires to look at a tag play at home plate, when Sean Rodriguez scored on a single by Guyer to give the Rays a three-run lead at the time. The call on the field was upheld, as Rodriguez touched the plate ahead of a tag from catcher Brian McCann.
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.