Justice delayed is justice denied.
—British Prime Minister William E. "Don't Call Me Ricky" Gladstone

The estimable Bob DuPuy denied the Indians protest of their 7-4 loss on April 28 to the Orioles. In the game, a botched call on a run scoring before the completion of a non-continuous double play caused a game erroneously tied 2-2 to become a retroactive 3-2 O's lead three innings later.

DuPuy reached his decision "because the umpires' mistake did not involve a judgment call, and because there is nothing in the Official Baseball Rules to address when umpires can make a correction, the umps can act at their own discretion."

I also would have mentioned that the delay did not affect the outcome of the game. The Indians went on to grab a 4-3 lead on a "Why Can't Jhonny Spell" Peralta homer in the sixth just after the run was posthumously added to the score. The Indians lost 7-4. So what would have been the difference if the 2-2 tie had been a 2-3 deficit for three innings? Would the Indians have tried that much harder to score a run from the third to the fifth? I think not. Why not blame it on the decision to use Aaron Fultz with the game on the line in the eighth.

Baseball's official statement cited "'the first requisite is to get decisions correctly,' [therefore,] this umpire crew was within the authority that Rule 9.01 (c) gave them to correct the game score when they did." I guess they can't say in an official statement that the umps involved are complete doofises.

Baseball's statement is based on the General Instructions To Umpires at the end of the Umpire section of the rule book (section 9):

Each umpire team should work out a simple set of signals, so the proper umpire can always right a manifestly wrong decision when convinced he has made an error. If sure you got the play correctly, do not be stampeded by players' appeals to "ask the other man." If not sure, ask one of your associates. Do not carry this to extremes, be alert and get your own plays. But remember! The first requisite is to get decisions correctly. If in doubt don't hesitate to consult your associate. Umpire dignity is important but never as important as "being right."

"Umpire dignity"? No that's an oxymoron. Unfortunately (and amazingly) here none of the umps, some seasoned professions like Ed Montague, knew this very basic rule. They didn't know they got it wrong until they bothered to check the rulebook three innings later. If I were a manager, I would have one of my coaches carry the rulebook (instead of tobacky) in his back pocket for just these sorts of situations.

Rule 9.01(c) is a quick one: "Each umpire has authority to rule on any point not specifically covered in these rules.". I love that one. It's perfect for giving boneheaded umps a Mulligan whenever needed. It's great that the baseball gods in formulating the rules of the game acknowledged Gödel's Theorem , which tells us that any system is inherently incomplete.

I couldn't find an example in which a decision, especially one that affected the score, was delayed for anything like three innings, but Rich Marazzi's The Rules and Lore of Baseball had an interesting one, though it was a shorter delay (I'll mercifully skip Merkle's boner):

In a game against the St. Louis Browns in 1922, with two out in the top of the ninth inning and the Yankees ahead 2-1, the Browns' Johnny Tobin grounded to Yankee first baseman Wally Pipp, with Chick Shorten on second and Pat Collins on first. Pipp tossed to Yankee chucker Sam Jones, covering first base. Umpier Ollie Chill waved Tobin out, and the Yankee players along with the large crowd of 49,152 assumed the game was over.
However, Lee Fohl, coaching at first, had noticed that Jones did not have possession of the ball as he juggled it before holding it securely. Fohl took it up with plate umpire Brick Owens, who told Chill in his opinion Tobin was safe. In the meantime, the tying Brown run had scored from second. After a 20-minute delay, Chill reversed his original decision, the game was resumed, and the Browns won, 7-2. So here we have a game that was temporarily won but eventually was lost.