Executive Vice President for Baseball Operations Joe Torre made the ruling, which stemmed from a play disputed by Rays manager Joe Maddon in Saturday's 5-4 loss to the Blue Jays in 10 innings.
Wil Myers was called safe at first base on a pickoff throw by Toronto pitcher Mark Buehrle. After Buehrle returned to the rubber, Blue Jays manager John Gibbons came out to challenge the call.
Myers was called out on a replay review, and Maddon told umpire crew chief Bob Davidson that he was playing under protest.
The replay rules say challenges must come before the next play or pitch. The rules say the crew chief decides whether a manager's challenge is timely.
"We got a couple of different interpretations where you can and cannot protest," Maddon said Tuesday at Camden Yards. "I didn't think we were protesting replay. We were protesting the right to go to replay. Again, it is what it is."
"I can sit here all day long and tell you how much I disagree with it. At the end of the day, as much as respect as I have for Joe Torre, for me it's over and done with. From my perspective, I hope the discussion continues because I think the whole situation deserves discussion," he said.
Regarding the use of replay, Maddon said, "It's going to be a fluid system and things are going to change. It's going to be worked out and it's going to become very good for the game. But what I don't get is the most clear, the clearest point of all, has been disputed and overturned. That's what I don't quite understand."
The struggling Blue Jays were obviously happy with the ruling.
"We might have been winless for the week if they'd nailed that thing," Toronto manager John Gibbons said. "Deep down I really had no worries that they were going to uphold that thing. To guarantee that in the win column always helps."
Asked whether the league asked him to make quicker use of the replay, Gibbons replied, "I'm sure I'll get a note saying, 'Speed it up a little bit better next time.' They'll leave no doubt maybe. They did the right thing. Bottom line, they got the call right. That's what the whole replay system is for anyway."
Last week, San Francisco became the first team since 1986 to win an MLB protest. The Giants contended a rain-shortened loss at Wrigley Field should've instead been a suspended game.
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