The 20-year-old Gotze, who will join Bayern at the end of the season, has been ruled him out of the Wembley showpiece after picking up a muscle injury in the semi-final against Real Madrid.
"When players like Gotze drop out, maybe the team gets a little weaker," Schweinsteiger said. "It would have been the biggest game of his career so I sympathise with him.
"However Dortmund will put out 11 players who will give 100 per cent for the cause," said Schweinsteiger, hoping that Bayern can secure the trophy for a fifth time this weekend.
"We respect Borussia Dortmund but I believe it's down to us if we win or lose," added Schweinsteiger. "If we reach our potential then there are only a few teams in Europe who can beat us."
Bayern are chasing an unprecedented treble after winning the Bundesliga in record fashion. They also take on Stuttgart in the German Cup final on June 1.