Wayne's agent, Joby Branion, confirmed the deal was completed but did not provide details about how much Indianapolis would save.
Players frequently restructure contracts by accepting bonuses after agreeing to lower their annual salaries. The bonuses are then prorated over the remaining length of the deal, in Wayne's case three years, to lower the team's salary cap number in the first year.
Wayne has been the Colts' primary receiver the past two seasons and is expected to play a more prominent role this year after Marvin Harrison, the franchise's career receiving leader, was released in February.
In 2007, Wayne had a career-high 104 receptions for a league-leading 1,510 yards and 10 touchdowns. Last season, Wayne caught 84 passes for 1,145 yards with six TDs.
He ranks third all-time on the Colts' career list for receptions (576), yards receiving (8,129) and touchdown receptions (53), trailing only Harrison and Hall of Famer Raymond Berry in each category. Only Harrison has more 100-yard games in franchise history than Wayne's 26, and Wayne has played in the last three Pro Bowls.