The Spaniard collided with Marcel Schmelzer in the first half of the DFL-Supercup match and initial reports claim he has ruptured his anterior cruciate ligament.
The Spaniard was involved in a collision with BVB defender Marcel Schmelzer shortly after Henrikh Mkhitaryan had given Jurgen Klopp's side the lead.
The former Athletic Bilbao man went down immediately clutching his knee and was unable to continue, being replaced by Dante shortly after.
Initial reports in Germany claim the Spaniard has ruptured his anterior cruciate ligament, but the club is yet to confirm the extent of the injury.
Guardiola had started the match with Martinez, a midfielder by trade, in a defensive role as Pep Guaridola looks to experiment with a 3-4-3 formation.