After playing in eight games, with three plate appearances, for the 1960 Cardinals, he was released as a player on August 5 and added to the coaching staff of manager Solly Hemus, then reappointed for 1961.

[5] He appeared in the 1961 World Series against his former team, the Yankees, and had two singles in four at bats (both of them off Baseball Hall of Famer Whitey Ford) as the Reds lost to the slugging Yanks of Roger Maris and Mickey Mantle, four games to one.

[6] The Reds released Johnson only a few days into the 1962 season, and he signed with the Orioles as a backup catcher before retiring as a player in June and serving out the year as Baltimore's bullpen coach.

His demotion was the result of an exchange requested by Red Wings president Morrie Silver, who was disappointed with a losing 1965 campaign and wanted the Pioneers' Earl Weaver, coming off a winning season, to manage his team instead.

[7] After a year spent scouting for the 1967 Yankees, Johnson was named pitching coach of the Boston Red Sox on October 31, 1967, succeeding Sal Maglie who had been released after the World Series.

In 1973, he became the first manager of the Triple-A Pawtucket Red Sox, finishing 78–68 and winning his second Governors' Cup, emblematic of the International League's playoff championship, in his only PawSox season.

In an interview conducted by Tim Russert on CNBC in 2003, Baseball Hall of Fame catcher Carlton Fisk named Johnson as the biggest influence in his professional life.

[11] Johnson also had his detractors, such as Bill Lee, who stated that the team won "despite our manager", who did not communicate well with his players and even had his pitching coach stationed in the Red Sox bullpen rather than the dugout during the 1975 Series.

But by then the Red Sox were mired in another slump, and only five days later on July 19, Johnson was fired in favor of third-base coach Don Zimmer after the team had lost eight of its last 11 games.