From BR Bullpen
Protested games are dealt with under section 4.19 of the rules. Only errors in the interpretation of the rules can be the object of a protest; judgement calls, such as the calling of balls and strikes, or calling a baserunner safe or out, cannot be protested. The manager must immediately inform the umpires of his intention to protest their ruling, and file a formal request for review with the league office within a specified time frame. The league will then rule on whether the umpires erred, and if the disputed action affected the outcome of the game. If the protest is upheld, the game is replayed from the point of the disputed ruling.
Protests are very rarely upheld in Major League Baseball. The most famous recent instance of a protest being successful is the July 24, 1983 Pine Tar Game, in which American League President Lee MacPhail ruled that umpire Tim McClelland was wrong to void a home run hit by George Brett with a bat that had more pine tar than allowed by the rules. The ruling meant that the home run was declared valid, and that the game was resumed on August 18, with the batter following Brett in the batting order batting with two outs in the 9th inning.
Another instance of a successful protest involved a May 15, 1975 game at Parc Jarry. The visiting Atlanta Braves argued that the umpiring crew did not wait long enough to call the game nor tested the playing field after a rain delay in the 4th inning. The successful protest meant that the game was resumed on July 20 from the point of the delay, with Atlanta leading Montreal 4-1, instead of being cancelled and having to be replayed in its entirety.
However, most protests are rejected, either because the league office agrees with the ruling on the field, or it finds that the mistake did not affect the outcome of the game. An example on June 21, 2009 involved the Florida Marlins making a double switch while batting in the bottom of the 7th inning, then sending one of the substituted players, Chris Coghlan, back to the outfield at the beginning of the 8th. New York Yankees manager Joe Girardi recognized the mistake, and came out of the dugout to point it out to the home plate umpire after a pitch was thrown. The umpires instructed Marlins manager Fredi Gonzalez to send in the correct player. The Yankees protested the game, but the league office ruled that having an ineligible player on the field for one pitch which was not hit did not substantially affect the outcome of the game, and the result - a 6-3 Marlins' win - was allowed to stand.