The midfielder was denied from the spot by his former team-mate and opted to make a quiet exit from the Veltins Arena after the game
Pierre-Emerick Aubameyang gave BVB the lead but Schalke were handed the opportunity to equalise 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 hosts.
"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% 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 team-mate having played with the keeper during a loan spell with BVB back in
"It is always difficult for the shooter to compete against an ex- team-mate," he added.
The result leaves Schalke in sixth place on 14 points and 11 points behind their fierce rivals, who trail leaders Bayern Munich by just a single point.