The defender scored with 18 minutes remaining as the reigning Bundesliga champions' poor start to 2015 continued on Tuesday evening
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.
The Bavarians - who made three changes from the defeat to Wolfsburg - dominated possession in typical fashion in the opening exchanges, but it was Schalke who wasted a golden opportunity to go ahead in the 18th minute.
Boateng clumsily brought down Sam inside the area and was shown a straight red card, but Choupo-Moting's tame spot-kick was easily saved.
Neuer was called into action again a minute later, parrying Sam's powerful drive from the edge of the box.
Schalke emerged for the second half having changed goalkeeper, with 19-year-old Timon Wellenreuther making his first senior appearance after Fabian Giefer was unable to continue with a hamstring injury.
The young keeper was tested 12 minutes after the interval, beating away a shot from Robben, who made space for himself with a darting run.
Wellenreuther was beaten 10 minutes later, though, as Bayern substitute Robert Lewandowski prodded a pass back into play from close to the byline, and the ball took a deflection off a defender before squeezing in at the near post.
However, much to the ire of Pep Guardiola, who ran down the touchline to remonstrate with the linesman, the officials decided the ball had gone out before Lewandowski's intervention.
But Bayern were not to be denied for long as, from the resulting corner, Robben headed in Alonso's cross via a slight deflection.
Yet their lead lasted just five minutes as Howedes rose highest to glance in Sam's corner and level matters, ensuring Bayern's wait for a win following the mid-season break goes on.