The league leaders were eager to get back to winning ways at the Allianz Arena following Friday's heavy defeat at the hands of Wolfsburg, but found themselves a man short after 17 minutes.
Jerome Boateng hauled down Sidney Sam inside the penalty area to earn a red card, although Manuel Neuer saved the resulting spot-kick from Eric Maxim Choupo-Moting .
Arjen Robben eventually opened the scoring for Bayern after 67 minutes, but they were denied a win as Benedikt Howedes levelled five minutes later.
"I'm not satisfied, I am very, very, very satisfied," said Bayern coach Guardiola, despite seeing his side drop points for a second successive game.
"Of course we wanted three points, but 70 minutes outnumbered against Schalke is not easy.
"We had the game very well controlled and had enough chances.
"Our performance was much better than in Wolfsburg. Everything is okay. The red card - no discussion! We were lucky that they have missed the penalty."
Bayern's lead at the top of the table remains eight points, though, after Wolfsburg failed to take their opportunity with a 1-1 draw at Eintracht Frankfurt.
