Jones went to Louisiana State University in Baton Rouge, where he played for LSU's football team. He was also a member of the Kappa Sigmafraternity (Gamma chapter). While at LSU, Jones only started two games prior to the end of his junior year, but he started every game after that, leading LSU to a 12-2-1 record. During his senior year (1972), LSU went 9-2-1. Except for one week, LSU spent that entire season ranked in the AP Top 10. That year, Jones became the first quarterback in LSU history to be awarded consensus All-American honors. Jones also finished 4th in the vote for the Heisman Trophy and was voted the National Collegiate Player of the Year by the Cleveland Touchdown Club.
One of Bert Jones' most famous moments came in the 1972 LSU-Ole Miss game, when he led LSU to a 17-16 last-second victory by hitting RB Brad Davis in the end zone for a touchdown as time expired. To this day,many believe that a clock malfunction on the previous play gave four seconds for Jones to complete the game winning touchdown pass for LSU. Jones's other major victories included #14 LSU's 28-8 victory over #7 Notre Dame in 1971 (televised by ABC) and #8 LSU's 35-7 victory over #9 Auburn in 1972.
During his 17 games at LSU, Bert Jones completed 52.6 percent of his passes for 3,225 yards and 28 touchdowns, which at the time was the most career passing yards and touchdowns of any quarterback in LSU history.
In 1971, Jones threw for 945 yards with 9 TD vs 4 INT while splitting time with Paul Lyons. Lyons himself would throw for over 800 yards and 11 TD that year. In 1972 after taking over command at QB, Jones threw for 1,446 yards with 14 TD vs 7 INT on 199 pass attempts.
Against the wishes of LSU fans, Jones was forced to share quarterback duties with Lyons because of Jones' bickering with head coach Charlie McClendon over signal calling.
In 1973, Jones was chosen in the first round (2nd overall) of the NFL draft by the Baltimore Colts to be the Colts' heir apparent to Johnny Unitas, who was later traded to San Diego. His debut came on September 16, 1973 in a loss to the Cleveland Browns. During his eight-year tenure as the Colts' starting QB, Jones and his teammates enjoyed three consecutive AFC East division titles (1975–77). But in each of those years, the Colts lost in the first round of the playoffs. The 1977 playoff game (known as Ghost to the Post) is famous as the 4th longest game in NFL history; the Colts fell to the Oakland Raiders, 37-31. The Colts' fortunes seemed to rise and fall with Jones; he missed most of 1978 and 1979 with a shoulder injury, and the Colts fell to last place in the AFC East those two seasons.
During an October 26, 1980 game against the St. Louis Cardinals, Jones made NFL history when he was sacked a record 12 times. This broke the record at the time held by many quarterbacks, including Jones' then back-up, Greg Landry, who had been sacked 11 times while he was a member of the Detroit Lions in a game against the Dallas Cowboys on October 6, 1975.
In 1982, his final season, he played in only four games for the Los Angeles Rams before a neck injury (OPLL) forced him to retire.
In 1990, Jones participated in the first NFL QB challenge. He finished first in the retiree category and third in the regular competition. (The regular competition taking the top three finishers from the alumni competition and adding them to the regular field of current QBs.) Given his strong performance, Bobby Beathard, then the GM of the Chargers, wanted Jones to come out of retirement, but Bert was 39 at the time and chose not to try a comeback.
The widely respected scout Ernie Accorsi is quoted as saying that if Bert Jones had played under different circumstances, he probably would have been the greatest player ever. John Riggins has been quoted as saying Bert was the toughest competitor he has ever witnessed. On the eve of Super Bowl XLII New England Patriots head coach Bill Belichick, in discussing his choices for the greatest quarterbacks of all time, described Jones as the best "pure passer" he ever saw.