Pierre-Emerick Aubameyang gave BVB the lead but Schalke was handed the opportunity to equalize when Christian Fuchs was fouled by Neven Subotic in the area.
However, Boateng saw his penalty saved by Weidenfeller, with Nuri Sahin and Jakub Blaszczykowski sealing the Ruhr derby spoils for Dortmund either side of Max Meyer's strike for the home side.
"The penalty is of course in my mind. I chose the wrong option. I really wanted to meet with Roman after the game, but I could not face seeing him," said the 26-year-old. "If the penalty would have been possible, the game could have been 100 percent different. Dortmund made the most of our mistakes."
Weidenfeller, 33, has now saved four of the last eight penalties he has faced and believes Boateng perhaps felt the pressure of facing a former teammate having played with the keeper during a loan spell with BVB.
"It is always difficult for the shooter to compete against an ex-teammate," he added.
The result leaves Schalke in sixth place on 14 points and 11 points behind its rival, which trails leader Bayern Munich by just a single point.