Maghoma has moved to Sheffield Wednesday this summer while Zola, who scored 16 goals in 38 games last season, has joined Aberdeen.
"The big question will be how much do we miss Jacques Maghoma and Calvin Zola," Rowett told BBC Radio Derby.
"That is the key difference - we are not going to get another Jacques Maghoma who is going to win you a game.
"Now I'm not going to say he did it single handed, because that is unfair on the rest of the players, but he came up with a little bit of magic more often than not."
The Brewers finished fourth in League Two last season before losing in the playoff semi-finals to Bradford City.