The Swans took a 1-0 lead through Darren Pratley just 40 seconds into the second half and looked to be leaving Devon with maximum points until Andrea Orlandi handled in the box from a Yannick Bolasie corner three minutes from time.
Swans keeper Dorus de Vries saved Jamie Mackie's resulting spot-kick but was adjudged to have moved off his line and Damien Johnson scored from the retaken penalty - albeit after de Vries had saved his spot kick but he had pounced on the rebound.
"Everyone in the ground could see what happened. I have watched a replay of it since and the keeper's foot is on the line," Sousa said after the 1-1 draw.
"Dorus did well to save them both and showed what he can do when he is called upon although we have not needed him for the past month or so.
"We dominated the game for long spells but we needed two or three touches on that pitch when normally we would only need one.
"We were not able to play the way we wanted and pass it quickly."