Rovers and Palace played out a hard-fought 1-1 draw at Ewood Park on Saturday and Holloway raged after the match, claiming Hanley was fortunate not to concede a second-half penalty for a challenge on Glenn Murray.
Bowyer took issue with the outspoken Bristolian's choice of words but also moved to draw a line under the issue.
"Following on from what was a competitive game and a well-earned point against a good Crystal Palace side, I was disappointed to read Ian's post-match comments," he told Blackburn's official website.
"It was a poor choice of word and we strongly refute the claims that Grant or any other player at this club would deliberately cheat.
"Grant is a young lad who has been outstanding for us this season. He should be commended for the consistently high level of performances he has produced this term and not pilloried for one challenge that was deemed acceptable by the match officials.
"Ian clearly felt his side should have been awarded a penalty, but we too felt that we were denied a stonewall penalty when Josh Morris was tripped in the box. We wish Palace all the best in their pursuit of the play-offs."