Boston got Higgins back in mid-1946 as the team's regular third baseman, winning the AL pennant by 12 games (but losing the 1946 World Series to the Cardinals in seven).

Although he had winning first-division teams through 1958 and Ted Williams won two more batting titles (1957–58), the Red Sox never seriously contended—never finishing less than 12 games in arrears of the first-place New York Yankees.

In 1959, with the 40-year-old Williams injured (and turning in the only sub-.300 season of his career), the Red Sox lost 42 of their first 73 games,[8] and on July 3, Higgins was replaced as manager by Billy Jurges, a coach with the Washington Senators (and former star shortstop of the Cubs in the 1930s).

[9] He hung up his uniform and joined Boston's front office full-time as executive vice president and general manager after the 1962 campaign, finishing his managerial career with a record of 560–556 (.502) in 1,119 games.

But apart from swapping shortstops with Paul Richards' Houston Colt .45s, acquiring Eddie Bressoud for Don Buddin, Higgins made no other significant trades during the remainder of his two-year (1961–62) tenure as both manager and supervisor of playing personnel.

Once he was named full-time general manager, in the autumn of 1962, he did make a few major trades, one of them netting slugger Dick Stuart from the Pittsburgh Pirates, but they did not materially improve the club on the field.

He made no further major deals until after the 1964 campaign, when he sent Stuart to the Phillies for left-handed starting pitcher Dennis Bennett, who suffered from a sore arm and would win only 12 games (losing 13) in 286+1⁄3 innings over 2+1⁄2 seasons in a Boston uniform.

The Red Sox continued to struggle at the major-league level, and in 1965 they lost 100 games for the only time during the Yawkey era for lack of pitching.

But meanwhile, in their farm system directed by Neil Mahoney, they were amassing talented young players (including African-American players such as outfielder Reggie Smith, first baseman George Scott and third baseman Joe Foy) who would lead them to an improbable AL pennant in 1967, aided and abetted by 22-game winner Jim Lonborg and Triple Crown winner Carl Yastrzemski.

Higgins, however, was finally ousted by Yawkey on September 16, 1965, ironically the same day 21-year-old Boston righthander Dave Morehead threw a no-hitter.

Red Sox historians often single out Higgins, along with Yawkey, when they discuss the root of the club's reputation for resisting racial integration.

The Red Sox' first African American player, utility infielder Pumpsie Green, was recalled from the minor leagues in July 1959, during Jurges' brief tenure as pilot.

But Higgins had no control over the big league roster until he became Red Sox manager in 1955, and the club's policy of refusing to break the color line appeared to be in place well before then under Yawkey and his front office bosses, Eddie Collins and Joe Cronin.