The German champions played with 10 men for 73 minutes following Jerome Boateng's sending off in the first half and the visitors' numerical advantage ultimately told.
Bayern came into Tuesday's meeting smarting from a 4-1 thrashing at the hands of Wolfsburg last time out, and it looked as though they would face another struggle when Boateng was sent off for a foul on Sidney Sam in the box inside the opening 20 minutes.
But Eric Maxim Choupo-Moting, who has 10 goals in all competitions this season, saw his weak effort saved by Manuel Neuer.
It seemed the visitors would be left to rue that missed opportunity when Arjen Robben headed in Xabi Alonso's corner midway through the second half, but Howedes produced a similar finish from Sam's set-piece in the 72nd minute to earn his team a share of the spoils.
Despite dropping points for the second time in succession, Bayern maintain their eight-point advantage at the top of the Bundesliga thanks to Wolfsburg's 1-1 draw at Eintracht Frankfurt.
