He became the starter at quarterback in the seventh game of his sophomore season, after passing Daniel Ford on the depth chart. He completed 56% (84 of 150) of his passes, threw for 1,063 yards, 5 touchdowns and 2 interceptions, while helping the team post a 6–5 record.
In 1989, he completed 33 of 47 passes for 534 yards (school-record) and 4 touchdowns in a 44–39 upset of No. 23 ranked Washington State University. He finished the season with a 6–4–1 record, 2,591 yards, 17 touchdowns and 10 interceptions.
In 1990, the Sun Devils opened the season with victories over Baylor University and Colorado State University, but would lose 4 consecutive games, 3 of them while Justin was out with a dislocated left shoulder suffered during a 30–9 loss against the University of Missouri. He also spent two days in a hospital with a probable case of appendicitis, that was later diagnosed as a gastrointestinal problem and caused him to lose 17 pounds. He posted a 4–7 record, 1,876 yards, 10 touchdowns and 10 interceptions.
In 1997, he started 4 games, while Harbaugh recovered from a fractured right hand he suffered when he scuffled with NBC sportscaster Jim Kelly. Against the Buffalo Bills, he was winning 26–0 in the first half, but the lead disappeared after the Bills outscored the Colts 30–3, Justin made it close again at 37–35 with 14 seconds remaining, but could not complete the potential game-tying two-point conversion. The Bills recovery from a 26-point deficit at the time was the second-largest comeback in NFL history. Coming in with an 0–10 record against the defending Super Bowl champions Green Bay Packers, he led the team to a 41–38 win, completing 24-of-30 attempts for 340 passing yards. On December 5, he was placed on the injured reserve list.