In 1971, Jones threw for 945 yards with nine touchdowns and four interceptions while splitting time with Paul Lyons. 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. Lyons himself threw for over 800 yards and 11 touchdowns that year.
In 1972 after taking over at quarterback, Jones threw for 1,446 yards with 14 touchdowns and seven interceptions on 199 pass attempts. Except for one week, LSU spent the entire season ranked in the AP Top 10. One of Jones' most famous moments came in the 1972 LSU vs. Ole Miss game, when he led LSU to a 17–16 last-second victory by hitting running back 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. After the season, Jones became the first quarterback in LSU history to be awarded consensus All-America honors. Jones also finished fourth in the vote for the Heisman Trophy and was named the national collegiate Player of the Year by The Sporting News.
During his 17 games at LSU, 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 school history.
Jones was projected by NFL scouts to be the first quarterback drafted in 1973. He was chosen second overall 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 quarterback, 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 fourth longest game in NFL history; the Colts fell to the Oakland Raiders, 37–31. Jones 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, Jones played in four games for the Los Angeles Rams before a neck injury forced him to retire.
In 1990, Jones participated in the first NFL Quarterback 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 quarterbacks). Given his strong performance, Bobby Beathard, then the general manager of the Chargers, wanted Jones to come out of retirement, but Jones was 38 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 Jones 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 had ever seen.