The former Leeds United midfield player has led the Londoners to two victories since taking temporary charge at The Valley following the departure of Karl Robinson to Oxford United.
Bowyer will be desperate to make it a hat-trick of wins today in a contest that pits the teams sitting eighth and fourth in the table against each other.
“They were a really good footballing side under Karl,” said Warne, whose side were held to a draw by another play-off challenger, Peterborough United, on Good Friday.
“Lee Bowyer has taken over, who was one of his coaches, so I don’t think a lot will have changed.
“What does change when a manager goes is that it gives the lads on the periphery a bit of an uplift. It is a different voice and training might be a little bit different.
“A change is as good as a rest and it will definitely re-galvanise them until the end of the season. He is inexperienced in coaching but he’s not inexperienced in the game.
“He is enthusiastic and it might just give them a different edge.”
Rotherham were desperately unlucky not to claim all three points against Peterborough after leading until the ninth minute of stoppage time.
Nevertheless, the draw maintained United’s eight-point cushion on the chasing pack in the race to finish in the top six.
Today, however, represents a chance to widen that gap against a team who are desperate to gate-crash the play-off places.
“I honestly believed that Charlton would have been pushing for an automatic spot,” said Warne, whose side lost 2-0 to today’s opponents when the two teams met at the New York Stadium in August.
“The season probably hasn’t gone the way they would have liked but it doesn’t deter from the fact that on their day they’re really difficult to play against.”
“I thought they came here and really dominated the ball. They made it really difficult for us to get around them.
“I think they were possibly the best team we have had here at Rotherham for that.”
Last six games: Charlton Athletic LLLDWW, Rotherham United WLLWLD.
Referee: G Horwood (Bedfordshire).
Last time: Charlton Athletic 1 Rotherham United 1; September 12, 2015; Championship.