Thomas made the Chiefs team as an undrafted free agent from Bishop College in Dallas; he was an AFL All-Star in 1968 and made the NFL's AFC-NFC Pro Bowl four times (1971, 1972, 1973, 1975) after the Chiefs joined the NFL in the 1970 AFL-NFL Merger. He was also selected All-Pro three times. In the 1969 season, he led all pro football with 9 interceptions, which he returned for 146 yards and a touchdown, helping his team win the AFL Championship and the fourth and last AFL-NFL World Championship Game, which the Chiefs won 23-7 over the NFL champion Vikings. Thomas recorded an interception in the Kansas City victory. In 1974, he led the NFL in interceptions (12), return yards (214), and return touchdowns (2).
Thomas retired from playing after 13 seasons; he finished his pro football career with 58 interceptions, which he returned for 937 yards and five touchdowns. He also recovered four fumbles, gained 64 yards returning punts, and returned 29 kickoffs for 673 yards. He played in 181 career games, tying for the fifth-most in club annals, and his 58 interceptions are a franchise record.
Thomas has been an assistant coach in the NFL since 1981. Before being named interim head coach of the Atlanta Falcons on December 12, 2007 after the resignation of Bobby Petrino, Thomas was the Falcons' Senior Defensive Assistant/Secondary Coach. After Petrino's sudden departure left the team in shambles, Thomas attempted to unite the Atlanta locker room, and was able to lead the Falcons to a season-ending victory over the Seattle Seahawks. On January 24, 2008, new Falcons head coach Mike Smith announced that Thomas would remain on staff as assistant head coach. Thomas was voted into the Pro Football Hall of Fame along with Darrell Green and Art Monk, two players he coached during Super Bowl runs with the Washington Redskins. On January 13, 2010, his contract expired and was not renewed by the Falcons.