Bratkowski was considered one of college football's greatest quarterbacks of his day and was the NCAA's all-time leading passer until 1961. Today, he still ranks sixth on Georgia's list of career passing leaders. Bratkowski also led the NCAA in punting his senior year in 1953 with a 42.6 yard average. He was selected for the North–South All-Star Game in Miami, Florida in December, and led the South to a 20–0 victory.
Bratkowski was selected 17th overall in the second round of the 1953 NFL draft by the Chicago Bears as a "future choice" after his redshirtjunior season, then played his fifth-year senior season at Georgia in 1953. He joined the Bears as a rookie in 1954. He started the first game of the season with a 64-yard touchdown pass, but was benched after completing just one of his next eleven passes with four interceptions. After George Blanda was lost for the season with a separated shoulder in mid-November, Bratkowski entered the game and threw three more interceptions in the loss. However, he started and won the last four games of the season, despite ten interceptions in those games for a franchise rookie record 17 on the season.
Bratkowski then served in the U.S. Air Force for two years, missing the 1955 and 1956 seasons. He returned in 1957 and shared time at quarterback with Ed Brown, and played five seasons in Chicago, through 1960. As of 2019[update], his seven interceptions in an October 2, 1960 loss to Baltimore remains a franchise record.
Bratkowski was traded to the Los Angeles Rams in March 1961, and played in Los Angeles for 2½ seasons before being signed in October 1963 by Vince Lombardi for the $100 waiver fee to become the "super sub" to Bart Starr. In Green Bay, Bratkowski was nicknamed "Uncle Zekie", and became an ideal backup and spot starter during the Lombardi championship era. In a 15-year NFL career, he passed for 10,345 yards and 65 touchdowns.
After coaching under Phil Bengtson in 1969 and 1970, Bratkowski came out of retirement to play again for the Packers in 1971 under first-year head coach Dan Devine, and appeared in six games, with one start. The following year, Bratkowski became an assistant coach for the Chicago Bears, a position he would hold for three seasons (1972-74); in 1973, the Bears activated Zeke as an emergency back-up quarterback for eight games, but he did not actually appear in any of them.
A superbly conditioned athlete, Bratkowski was an early advocate of aerobic training for pro football players.
After his playing career, Bratkowski became quarterback coach/offensive coordinator for Chicago, Baltimore / Indianapolis, Philadelphia, and New York Jets. He was also a quarterbacks coach with Cleveland and the Jets and worked two stints as a Green Bay assistant as well as the Baltimore Ravens.
While Bratkowski was coaching the Chicago Bears quarterbacks during the 1973 season, head coach Abe Gibron abruptly promoted him to offensive coordinator, then pressed him into service as a back-up quarterback (see above).