Barca have already qualified in first place from their group.
"Internal decisions will remain internal," Valverde said at a press conference when asked about the Ballon d'Or winner.
"These decisions are made by the coach based on what he believes is best.
"We are coming off the back of a number of games and, taking into account what we have coming up, we decided he couldn't come.
"When there is no Messi, there are still 11 players.
"For us, he is decisive, but it isn't the first time he is missing.
"Our goal is to maintain our competitiveness and style of play.
"Jordi Alba doesn't have the medical all clear, neither does [Nelson] Semedo and Messi has been rested.
"Neto will play tomorrow and that's all."