Argentina captain Messi has started in five of Barca's six games this season, but was forced off in Wednesday's 1-1 home draw against Atletico Madrid with a groin injury that will keep him out of action for three weeks.
The 29-year-old will miss Argentina's World Cup qualifiers in Peru on Oct. 6 and at home to Paraguay five days later, the Argentina Football Association (AFA) said in a statement.
"We all have to look after Lionel because he is at a stage where you have to manage his playing time," Bauza told Spanish radio Cadena Cope. "He has played five games in the last two weeks.
"Barcelona, who had the player most of the time, need to manage his time more.
"The reality is that Lionel has played one game for the national team in the last four months and that was against Uruguay."
Prior to the Uruguay game on Sept. 1, Barcelona had warned Argentina that Messi had a left adductor problem, but he played in the World Cup qualifier and scored the game's only goal.
He was then left out of the Argentina side that drew 2-2 in Venezuela five days later after Bauza decided to rest him on the advice of the club.
He returned to Barcelona, however, and played four club games in 11 days, the last of which was against Atletico.
"He should have played against Venezuela," Bauza said. "However, I opted to look after him and rest him following the recommendations given by Barcelona's medical team.
"Now he has gotten injured. I don't want to fight with Barcelona.
"We just want Lionel to recover and return to play for Barcelona and for the national team."
Argentina are third in the South American World Cup qualifying standings, one point behind leaders Uruguay after eight games.
(Reporting by Adriana Garcia; Editing by Toby Davis)
