Messi had felt pain in his thigh during Barca's draw against Valencia on Sunday and, despite training on Tuesday evening, was not deemed fit enough to start the first leg at the Camp Nou.
"There is still one practice session left, we'll see how he's feeling", Barcelona coach Ernesto Valverde said.
He is very important for the team as some of the results of the team without him prove, but let's not forget Barcelona have beaten Real Madrid by 5-0 this season in his absence.
On the Copa del Rey encounter with Real Madrid, the Barcelona boss added: 'It's a special game.
"In football it is good for the best players to play in all games", Solari said. "If Messi's ready he will play, if he's not he won't".
Real Madrid coach Santiago Solari said the uncertainty about Messi wasn't affecting his team's preparations.
Meanwhile, Los Blancos reached the last four, after securing an emphatic 7-3 aggregate victory over Girona. Asked about the fitness of Messi, he said: "It's always better when the best players get to play, it's as simple as that".
Bale is one of the many Madrid players who have recovered from injury in recent days, along with other forwards Mariano Diaz and Marco Asensio.
That could lead to some fringe players being given a chance to shine at the Nou Camp - with the likes of Brahim Diaz, Isco and Marcos Llorente hoping for the call.
Barcelona are among the clubs to have been linked with a move for the 26-year-old, along with the likes of Manchester City and Juventus, and Bartomeu would be happy to negotiate a deal with opposite number Florentino Perez.
He has been a regular in their Copa del Rey campaign, though, meaning he could come up against Barça on Wednesday.