The German said he did not feel fit enough for a complete race distance as he recovers from a pre-season crash in January which forced him to miss some testing at Barcelona.
He has been replaced by the team's third driver Antonio Giovinazzi, who is set to make his F1 debut in Sunday's Melbourne race.
"My fitness level is not as it should be for a full race distance because of my training deficit," Wehrlein said.
"I explained the situation to the team last night. Therefore, the Sauber F1 Team has decided not to take any risks. It is a pity, but the best decision for the team."
More From This Section
"We have great respect of Pascal's openness and professionalism," Kaltenborn said.
"This decision was definitely not an easy one for him, it underlines his qualities as a team player.
"The focus is now on his fitness level, and in such a situation we do not take any unnecessary risks."
He added that Wehrlein planned to be ready for the second race of the year in China.