Leon Goretzka and Javi Martinez will miss Saturday's home game against Hoffenheim at the Allianz Arena, with Bayern Munich seven points clear in the Bundesliga table.
UEFA Super Cup: After Lucas Ocampos converted an early penalty for Sevilla, Leon Goretzka equalised for Bayern, who had two second-half goals disallowed before substitute Javi Martinez, 32, struck from a late corner.
Bayern Munich extended their advantage at the top of the Bundesliga after defeating Schalke on Saturday.
Bayern Munich's Spanish international Javi Martinez required lengthy medical treatment on his knee after landing awkwardly following a tackle by Dortmund defender Marcel Schmelzer on Wednesday.
Teams coached by Pep Guardiola and Jose Mourinho have now met on 16 occasions with five draws and three victories for Mourinho with Guardiola's teams have scored 28 goals to Mourinho's 18.
Spain's Fernando Torres' early strike had been cancelled out by Franck Ribery's second-half thunderbolt while Chelsea's Ramires was dismissed in the 85th minute as it finished 1-1 after 90 minutes at Prague's Eden Arena. Eden Hazard looked to have hit an extra-time winner for Jose Mourinho's Europa League winners before Javi Martinez's 121st-minute equaliser.
Croatia striker Mario Mandzukic gave Bayern the three points at Eintracht, when he volleyed home a cross from Germany's Thomas Mueller on 13 minutes.
Munich coach Pep Guardiola gave Goetze 30 minutes off the bench in a friendly at Hungarian champions FC Gyor.
Although Arsenal were knocked out of the FA Cup on Saturday after their 1-0 defeat at home to Championship side Blackburn Rovers, Heynckes said he expects a tough match against the Gunners in London.
Bayern Munich's Spain midfielder Javi Martinez was on Saturday given the all clear after temporarily losing sight in his left eye in the 1-1 draw with Borussia Moenchengladbach in the Bundesliga.