Characterized by his soft hands, strong arm, and fiery personality, he won two Gold Glove Awards and led the National League in fielding percentage six times, then a league record. He retired with the NL record for career games at shortstop (2222) and the major league records for fielding average in a career (.980) and a single season (.991, in 1979), and was also among the career leaders in assists (6th, 6857) and double plays (4th, 1265); his records have since been broken, though he retains the NL mark for career fielding average.

Apart from his fielding achievements, he was a switch-hitter, batting .280 or better four times (.305 in 1975); he also had nine seasons with 20 or more stolen bases. From his 1970 rookie season through 1981, Bowa provided solid reliability in the Phillies' infield, along with third baseman Mike Schmidt; from 1976 to 1981, the Phillies reached the postseason five times, ending a drought dating back a quarter of a century. Bowa batted .333 in a losing cause in the 1978 NLCS, but played an even greater role in 1980, hitting .316 in the NLCS and .375 in the World Series as the Phillies captured the first title in franchise history. In 1979, Bowa set a major league record for shortstops with a .991 fielding average; Tony Fernández broke the record with a .992 mark in 1989, and Rey Ordóñez broke the NL record with a .994 average in 1999.

In January 1982, Bowa was traded to the Chicago Cubs along with rookie Ryne Sandberg in exchange for Ivan DeJesus, a move made by new Cubs general manager Dallas Green, who had managed the 1980 Phillies. The trade paid off tremendously for the Cubs, as Bowa's veteran leadership and Sandberg's outstanding all-around play brought the Cubs to the postseason in 1984 for the first time in 39 years. After being released by the Cubs in August 1985, Bowa played briefly for the New York Mets before retiring. He was a .260 career hitter with 15 home runs, 525 RBI, 2191 hits, 987 runs, 262 doubles, 99 triples, and 318 stolen bases in 2247 games. His NL records for career games at shortstop and most years leading the league in fielding were later broken by Ozzie Smith; his major league record for career fielding average has been broken by Omar Vizquel.

After retiring, Bowa was named manager of the San Diego Padres in 1987, but his aggressive and often angry style were ineffective, and he was fired a year later. Bowa returned to managing the Phillies in 2001, and was honored as Manager of the Year after bringing the team within two games of the division title; they had finished in last place in 2000. He quit with two games remaining in the 2004 season after failing to finish within 10 games of first place in his last three years.

After leaving the Phillies and before accepting his current job with the Yankees, Bowa served as an analyst for ESPN's Baseball Tonight and co-hosted a baseball talk show on XM Radio.