Instead, he was signed as a free agent by the Miami Heat where he was part of the 2005–06 NBA championship team. His scoring took a toll as he had a lesser role on this elite team. His scoring average dropped down to 4.1 for the season, and he only played 51 games in the season. But he won his first and only championship with the Heat. In the 2006–07 season, Kapono's points-per-game average and minutes played significantly increased, and he led the league in three-point percentage with .514, which is close to the all-time single-season three-point percentage record held by Kyle Korver (.536), and is the fourth best percentage in league season history. He averaged a career high in scoring, minutes, and rebounding. Kapono also won the Three-Point Contest in the 2007 All-Star Weekend three-point shoot-out competition by defeating Dirk Nowitzki and Gilbert Arenas in the final round with a score of 24 points which tied Mark Price's record for most points in a final round of the three-point contest. The 2006–2007 season is greatly considered to be the greatest season of his career due to his accomplishments and statistics. Despite this, the defending champions had a disappointing season, finishing with an average 44–38 record and getting swept in the first round by the Chicago Bulls.