On July 13, 2012, he was waived by the Rockets using the league's amnesty clause to provide salary cap relief. It was widely noted, however, that Scola was not cut due to a lack of performance; rather, the deal was an attempt to clear cap space for the Rockets to trade for former Orlando Magic All-Star center Dwight Howard. Howard was instead traded to the Los Angeles Lakers, but the Rockets used their cap space to gain former Oklahoma City Thunder Sixth Man of the Year shooting guard and Olympic gold medalist James Harden.
On July 15, 2012, Scola was claimed off amnesty waivers by the Phoenix Suns. Reportedly, the Dallas Mavericks and the Cleveland Cavaliers were also interested in acquiring him during the amnesty process. On November 21, 2012, he was relegated to playing off the bench for the first time in his NBA career since the start of his rookie season. He regained his starting spot less than a month later, and on December 29, he scored a season-high 33 points against the Minnesota Timberwolves. While Scola did become a leader for the Suns, he finished the season with declining averages, as his 12.8 points per game were his lowest since the 2008–09 season.