Nathan had a strong season, as he was selected as an All-Star for the 2009 MLB All Star Game, and he finished the year with 2.10 ERA with 47 saves in 52 opportunities, which was a franchise record. He shared honors for the AL Rolaids Relief Man award with Mariano Rivera. However, Nathan did not fare as well in the postseason; in Game 2 of the American League Division Series against the New York Yankees, with the Twins leading 3–1 in the bottom of the ninth inning, Nathan blew the save when he surrendered a game-tying two-run home run to Alex Rodriguez. It was the first home run Nathan had allowed with men on base all year. The Yankees later won the game in the 11th inning and swept the series. On October 11, 2009, after the Twins lost the final game at the Metrodome (a 4–1 playoff loss to the Yankees that eliminated them), Nathan took a pile of dirt from the mound as a keepsake from the Metrodome.