Bayern, looking to bounce back from last week’s shock 4-1 loss to Wolfsburg, were stunned when Jerome Boateng was contentiously sent off for bringing down Sidney Sam to concede a penalty after 16 minutes.
Manuel Neuer comfortably saved Bundesliga top scorer Eric Maxim Choupo-Moting’s weak spot-kick but Bayern, who dominated possession despite their numerical disadvantage, had further reason to complain in the second half.
Robert Lewandowski appeared to have taken advantage of a defensive mix-up to squeeze the ball in off Atsuto Uchida from the byline only to see the assistant referee on the far side signalling the ball had gone out of play first.
Replays were inconclusive but Bayern went ahead from the resulting corner as Arjen Robben headed home from Xabi Alonso’s cross in the 67th minute.
But it was not enough as Schalke hit back five minutes later with Howedes heading in a corner from Sam, securing a point for coach Roberto di Matteo on his return to the ground where he won the Champions League with Chelsea.
Second-placed Wolfsburg failed to take advantage of Bayern’s latest slip-up and needed a last-gasp Kevin de Bruyne equaliser to avoid defeat at Frankfurt.
Stefan Aigner put the hosts ahead at the Commerzbank Arena after 58 minutes as he finished off a quick break by firing in from Takashi Inui’s pass.
The Wolves – for whom new signing Andre Schurrle did not feature – fought back and levelled in the 88th minute when De Bruyne tucked in his sixth of the campaign from a Marcel Schafer cross.
Third-placed Borussia Monchengladbach gained some ground with a 1-0 win over Freiburg at Borussia-Park.
Patrick Herrmann claimed the only goal of the game after 23 minutes, volleying in after Fabian Johnson failed to connect with a cross from a Branimir Hrgota cross.
Freiburg went on to dominate possession and create the greater number of chances but could not find a way past Yann Sommer.
Hannover and Mainz played out a 1-1 draw in the night’s other clash at the AWD Arena.
Jimmy Briand opened the scoring for Hannover following a corner in the 26th minute.
Elkin Soto levelled 13 minutes from time moments after Hannover goalkeeper Ron-Robert Zieler had saved from Daniel Brosinski.