Philadelphia 76ers (1978–1986)
After the 1977–78 campaign Jones was traded to the Philadelphia 76ers alongside Ralph Simpson for forward George McGinnis with both teams exchanging draft picks and both Jones and McGinnis waiving their no-trade clauses. The trade came with a clause that should Jones be disabled due to epilepsy, the 76ers would receive a draft pick. There he joined a team that was coached by another UNC alum, former forward and future NBA Hall of Famer Billy Cunningham. On March 7, 1979, he scored a career-high 33 points. That season, they won 47 games as he averaged 12.5 points, 6.5 rebounds, 2.5 assists, 1.3 steals, and 1.2 blocks per game, and led the league in field goal percentage. He was also selected to the First-Team All-Defense once again.
Primarily a starter during his four seasons with the Nuggets, Jones made another transition after his first year with the Sixers. Coach Cunningham thought Jones would be best utilized as a sixth man, coming off the bench for the frontline Julius Erving, Darryl Dawkins, and Caldwell Jones. Cunningham was worried that the change would devastate Jones, but it took Jones about half a minute to agree to the coach's plan.
Beginning with the 1979–80 campaign, Jones still averaged about 25 minutes. He also scored 14.4 points in his first season off the bench, his highest scoring average in his time with the Sixers. They won the Eastern conference championship but lost in the 1980 NBA Finals to the Los Angeles Lakers in six games that season.
He returned to the NBA All-Star Game in 1981 as he was voted in by the coaches. Their season ended on a one-point loss to the Boston Celtics in the Eastern Conference finals.
In 1981–82, Bobby Jones briefly returned to the starting lineup for that season, starting 73 games. He was an All-Star again that season. They avenged their loss to the Celtics the previous season in an Eastern Conference finals rematch, but lost once again to the Lakers in six games.
The arrival of star center Moses Malone from Houston for Caldwell Jones prior to the 1982–83 campaign was seen as a gamechanger for the Sixers' title hopes. In the regular season, they went on a 14-game win streak, and won 65 games. Bobby Jones finished the season third in the league in defensive box plus-minus.
In the playoffs, the 76ers began with a sweep of the New York Knicks, although each game was decided by fewer than 10 points. In game one of the conference finals, the Milwaukee Bucks led by 109–108 with one minute 36 seconds to go in overtime. Alton Lister of the Bucks tried to inbound the ball but Jones stole the pass and flipped the ball to Clint Richardson. Richardson scored on a dunk to send the 76ers ahead 110–109. A Philadelphia Inquirer article on Jones paraphrased the famous John Havlicek call by Johnny Most stating, "Bobby Jones stole the ball. It was grand larceny. Bobby Jones stole the ball and robbed the Milwaukee Bucks of a game, turning an almost-sure upset into a 111–109 overtime victory for the 76ers." In Game 2, he had a crucial block on Brian Winters that helped seal the win for the 76ers.
After a Game 4 loss to Milwaukee, Philadelphia then rolled through the rest of the playoffs, eventually sweeping the Lakers in the 1983 NBA Finals. After the season ended, Jones won the first-ever NBA Sixth Man of the Year Award. From the Eastern Conference finals to the NBA Finals, he averaged 1.7 steals and 1.9 blocks.
The Sixers began a steady decline after that championship year, finishing second to Boston the next three seasons. While Jones continued to play steady defense, his offense began a gradual tail-off with reduced playing time and productivity. In the 1985–86 season Jones only averaged 6.6 points per game despite returning to the starting lineup, but still shot a highly efficient .559 from the floor. That season, Philadelphia was eliminated by the Bucks in the playoffs.
Jones retired shortly afterward, on November 7, 1986, at age 34. The Sixers retired his uniform No. 24.
In his 12-year professional career, Jones was named to the NBA All-Defensive First Team eight times and the Second Team twice; earned the first-ever NBA Sixth Man Award; was on the ABA All-Rookie Team; was a four-time NBA All-Star and one time in the ABA; and won an NBA Championship with the Philadelphia 76ers, in 1983. Over his career, he averaged 12.1 points and 6.1 rebounds, and his teams never missed the playoffs.