Rodriguez homered off Detroit's Justin Verlander on June 19, becoming the 29th player to reach the 3,000-hit plateau.
Rodriguez said he was ''in disbelief'' upon learning of the planned celebration.
Manager Joe Girardi said he was pleased to see the Yankees pay tribute to A-Rod's achievement.
''All relationships are going to have rocky moments and you like to see things get righted and repaired,'' Girardi said before Friday night's game in Toronto. ''I think both sides have made a lot of gestures to do that.''
Rodriguez missed all of last season while serving a drug suspension. Last month, Rodriguez and the Yankees settled a dispute over a marketing payment with a deal that gave $3.5 million to charitable groups.
Rodriguez is batting .264 with 24 homers and 63 RBIs in a resurgent season. He began the day in an 0-for-11 skid.