Kevin Grosskreutz's opener was cancelled out by Mario Gomez before Robert Lewandowski missed a penalty for the hosts.
Rafinha was sent off for Bayern in a game which did not lack drama, but went short of a winner, which will not be the case when the two teams meet again later this month in London.
The warm-up for the Champions League final on 25 May started with fewer than half of the players on the field who are likely to line up at Wembley.
Dortmund coach Jurgen Klopp was without the injured Mario Gotze, but he also gave a rest to Mats Hummels, Lukasz Piszczek, Sven Bender and Marco Reus.
Bayern boss Jupp Heynckes made even more changes to the side which defeated Barcelona in midweek, but in Claudio Pizarro and Gomez, he still fielded the two most prolific strikers currently in action in the Bundesliga.
Klopp had even said that defeat to Bayern would be one of the sweetest he would have ever experienced, but there was no sign his team were going to roll over and let the side who will take their Bundesliga title off them next weekend get away with another win.
They took the lead in the 11th minute when Nuri Sahin's sweeping ball forwards sent Jakub Blaszczykowski free down the left and his cross was met by Grosskreutz, who left Manuel Neuer with no chance on the volley.
The lead lasted only 12 minutes, though, before Gomez levelled with a header from Rafinha's cross.
Dortmund had the chance to regain the lead on the hour mark when Jerome Boateng handled the ball inside the penalty area.
Lewandowski stepped up, but Neuer guessed right and made a save low down to his left.
Rafinha then picked up two yellow cards in the space of three minutes to be given his marching orders, but as the tempers flared both on and off the field, with Klopp having to be separated from Bayern's director of sport Matthias Sammer, neither side could find a winner.
Reus was sent on to help the Westphalians find it, but despite a few interesting balls into the area, even he could not carve out a winner as both sides now begin preparations in earnest for their next meeting in three weeks' time.