The early 1960s Yankees responded to Houk's leadership; the 1961 team led by Roger Maris (61 home runs), Mickey Mantle (54 homers) and Whitey Ford (25 victories) won 109 games and beat the Cincinnati Reds in five games in the World Series. His 1962 club won 96 games, and were victorious over the San Francisco Giants in seven games in the Fall Classic. In 1963, the Yanks won 104 games and rolled to the pennant, but were swept in four games by the Dodgers in the Series.
Houk moved into the Yankees' front office as general manager on October 23, 1963, replacing Roy Hamey, and Berra, at the end of his playing career, became the Yanks' new manager. Yogi would win the 1964 pennant after a summer-long struggle with the Baltimore Orioles and Chicago White Sox, but Houk and the Yankee ownership quickly became disenchanted with Berra's work and in late August they made up their mind to fire him regardless of how the season turned out. After the Yankees' seven-game loss to the St. Louis Cardinals in the 1964 World Series, Houk sacked Berra. Later, Houk said that the Yankee brain trust had concluded Berra wasn't ready to be a manager, though he didn't elaborate on the reasoning.