Mark Simon, a stats guru at ESPN Stats & Information, passes along this list of those in the past 25 seasons that have had perfect games broken up with two outs in the ninth inning.
Yu Darvish was the fifth. Here are the other four:
Armando Galarraga, 2010 Tigers vs. Indians (6/2/2010, Jason Donald broke it up)
Mike Mussina, 2001 Yankees vs. Red Sox (9/2/2001, Carl Everett)
Brian Holman, 1990 Mariners vs. A's (4/20/1990, Ken Phelps [homer])
Dave Stieb, 1989 Toronto vs. Yankees (8/4/1989, Roberto Kelly [double])