Had a MLB game ever been forced to be replayed or the score ammended after the Commisioner reviewed a protest?

Answer 1

It was called the Pine Tar Incident.

http://en.wikipedia.org/wiki/Pine_Tar_Game

Answer 2

Not really, none that I know of, though Brett's Pine Tar game comes pretty close.

Short recap:
Brett hits top of ninth, go-ahead homer with two outs.
Martin points out Brett's bat has too much pine tar.
Umps agree, call Brett out, negate the runs scored, game apparently ends with a Yankee victory.
(Brett goes hyperballistic, which has nothing to do with how the game played out but is the signature moment.)
AL president (not commissioner) reviews incident, decides that (a) umpires made the wrong call (the rule book says the bat is ineligible, but there's nothing about the batter being called out) and (b) while the pine tar on the bat did violate the letter of the rules, it did not violate the spirit, and the home run should stand and the game continue.

The ending of the game was scheduled for an off-day for both teams. The Royals flew to NYC -- Brett stayed on the plane -- and the game resumed, with several amusing defensive substitutions (Martin demonstrating his protesting of the decision -- e.g., Mattingly at second base, Guidry in center).
Top of ninth was completed, bottom of ninth followed, pretty much nothing happened, and the 5-4 score following Brett's homer stood as the final.

Weird, weird game.

Box: http://www.retrosheet.org/boxesetc/1983/B07240NYA1983.htm

Answer 3

I don't think so. The first time replay was used to reverse a call was 5/31/99 when a home run was taken away from the Marlins while playing the Cardinals.