He played eight seasons (1980–1987) with the Steelers, becoming the fourth-ranked quarterback in franchise history at the time with 8,582 yards.  His highlights with the Steelers included giving the eventual Super Bowl Champion 49ers its only loss in 1984, and guiding the Steelers to the 1984 AFC Championship Game against the Miami Dolphins. He was traded on April 12, 1988, to the San Diego Chargers for his last, full NFL season. He would play one more game in 1989 with the New York Jets. For his career Malone passed for 10,175 yards and 60 TDs, and rushed 159 times for 628 yards and 18 TDs. Malone also had one career reception for a 90-yard TD, a Steelers team record until Mike Wallace broke it with a 95-yard touchdown reception vs. Arizona in 2011. Malone's career, however, was plagued with several severe injuries.
A September 1987 Sports Illustrated article on Malone recounted the knee injury he suffered against Chicago while playing wide receiver that forced him to miss the entire 1982 season after having surgery. Malone started only half the season in 1985 for Pittsburgh due to various injuries, and missed two games at mid season in 1986 with a thumb injury on his throwing hand.
Among his more memorable games in the NFL include becoming the first quarterback in Steeler history to complete over 80% of his passes (minimum 20 attempts) in a game vs. San Diego on November 25, 1984 (18 completions in 22 attempts, 253 yards, 4 touchdowns, 1 interception); won AFC Offensive Player of the Week for his opening day 1985 performance vs. Indianapolis (21 completions in 30 attempts for 287 yards, 5 touchdowns passing, 1 rushing) that included tying Hall of Famer Terry Bradshaw's team record for single game touchdown passes; passed for a career-high 374 yards on 26 completions with three touchdowns vs. Cincinnati on September 30, 1985; was the starting quarterback when Pittsburgh became the first visiting team to beat the Denver Broncos in the post season, leading the Steelers to a come from behind 24–17 victory in the 1984 AFC Divisional Game on December 30, 1984 (overcame two early fumbles to complete 17 of 28 passes for 228 yards and threw the game-tying touchdown pass to Louis Lipps); earned the final victory of his career as a starting quarterback against Pittsburgh, completing 17 of 24 passes, throwing a touchdown and scoring 1 rushing to lead San Diego to a 20–14 win over Pittsburgh on December 11, 1988; set a Steeler post season record (since eclipsed by Neil O'Donnell and Tommy Maddox) for single-game passing-yards for his 336-yard performance vs. Miami in the 1984 AFC Championship Game (completed 20 of 36 passes; threw 3 touchdowns and 3 interceptions).