The five-time Ballon d'Or winner has been sidelined since limping off during his side's 1-1 draw with Atletico Madrid on September 21, missing the club's last three matches in all competitions.
The 29-year-old will also miss his country's upcoming World Cup qualifiers against Peru and Paraguay, although Bauza insists that it was never an option to include the forward in his squad.
"Messi is worried about his injury. He wants to play games and it's difficult to be without him. We never toyed with the option of having him in this squad. We have to be careful together. Barcelona's medical staff know perfectly what he has to do, I simply say that he has to look after himself," Bauza told TyC Sports.
"He's now in the recovery process, which is good news. I think he'll be at a good level when he returns. I still say we should all take care of Messi. Here in Argentina he played only one game in three months. We don't have the best attacking player there is, so you have to put other options in to find that cutting edge. Argentina can find it, because we have very good players.
"The idea is that Gonzalo Higuain, if he is fit, will play as the number nine and Sergio Aguero will play behind him. [Paulo] Dybala could play instead of Messi on the right. Dybala can play Messi's role, given his position and numbers. Paulo is a player who can break the balance of the game."
Messi initially retired from international duty following Argentina's Copa America final defeat to Chile earlier this year, only to reverse his decision.