Fellow Springbok Jean-Luc du Preez is also out injured, the Sharks said on Monday.
Mtawariwa, 33 and with more than 100 international caps, had been named to play against the Stormers in Cape Town last Saturday but pulled out before kickoff with what the Sharks described as "knee niggle".
The Sharks secured a last gasp 12-9 victory to reach the playoffs and face the Brumbies, who won the Australian conference, but the absence of powerful scrummager Mtawariwa is a setback to the South African team's chances.
Flyhalf Curwin Bosch, who also missed the Stormers game, is fit again and travelled with the team.
(Writing by Mark Gleeson; Editing by Ken Ferris)
