Late in the season, Holmes replaced Cedrick Wilson in the starting lineup and finished the 2006 regular season with 49 receptions for 824 yards and 2 touchdowns. His best play of the season was also the last, when, in overtime of the Steelers' final game of the season against the Cincinnati Bengals, Holmes caught a pass from Ben Roethlisberger on a slant route and ran for a 67-yard touchdown to secure a win for the Steelers. He also returned a punt 65 yards for a touchdown on December 17 against the Carolina Panthers.