After joining the Yankees, Boyer spent the better part of three seasons in their farm system until he was called up late in . He became the Yankees' regular third baseman in , beating out three others (including Gil McDougald, who had announced in spring training that this, his tenth season in the majors, would be his last) for the starting job. He batted .242 with 14 home runs and 46 RBIs as the Yankees won the pennant. However, he had a humbling moment in the first game of the World Series against the Pittsburgh Pirates. With two runners on base and the Yankees trailing 3–1 in the second inning, manager Casey Stengel, never confident in Boyer's hitting, replaced him with pinch-hitter Dale Long, who flied out to right fielder Roberto Clemente. The Yankees didn't score in the inning and lost 6–4, ultimately losing the Series in Game 7 on Bill Mazeroski's home run off Ralph Terry in the bottom of the ninth. Boyer didn't play in the Series again until Game Six.