Born and raised in Westville, Illinois, Bratkowski played high school football at Schlarman Academy in Danville and graduated in 1949. He came to national prominence in his sophomore season at the University of Georgia in Athens in 1951, and was twice the SEC passing leader under head coach Wally Butts. During his three-year career with the Bulldogs, he completed 360 passes for 4,863 yards.

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 redshirt junior 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 11 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, 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.

In the Western Conference playoff game versus the Baltimore Colts in 1965, Bratkowski relieved the injured Starr early in the game and led the Packers to a 13–10 overtime victory on December 26 at Lambeau Field. The Packers went on to win the NFL championship game against the Cleveland Browns on January 2, 1966. This was the first of three consecutive NFL titles for the Packers, unprecedented in the playoff era (since 1933), and yet to be repeated.

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.

Bratkowski is a member of numerous halls of fame. In 1980, he was inducted into the State of Georgia Sports Hall of Fame. Nine years later (in 1989), Bratkowski was inducted into the Green Bay Packers Hall of Fame. He also was elected to the National Polish-American Sports Hall of Fame in 1995. Bratkowski was inducted into the University of Georgia’s Circle of Honor in 2006, and was the first member of his high school’s Hall of Fame in 1974.

Bratkowski died at his home in Santa Rosa Beach, Florida on November 11, 2019 of a heart attack at the age of 88.