Schalke had to settle for the point, but moved up to 54 points, nine adrift of leaders Borussia Dortmund and six behind Bayern Munich.
"I am very disappointed because I expected a different performance from my team," Schalke coach Huub Stevens said.
"Our defeat to Bilbao cannot be an excuse because professionals must be in a position to play three games in a week", he said referring to their 4-2 Europa League quarter-final home leg defeat by Athletic in midweek.
Sejad Salihovic had given Hoffenheim an unexpected lead with a well-taken penalty in the 31st minute with Schalke having looked far more aggressive at the start.
The visitors fought back and grabbed a deserved point with a spot kick of their own as Hoffenheim failed to win at home for yet another week with their last victory on their own ground stretching back to October.
Schalke's controversial penalty came after Chinedu Obasi fell in the box following a challenge from Andreas Beck in the 80th minute, seconds after Huntelaar had hit the bar.
The Dutchman quickly made amends, converting the spot kick for his 23rd goal of the season to join Bayern Munich's Mario Gomez at the top of the goal chart.
The top three teams automatically book a spot in the Champions League group stage for next season.