The double-amputee, 27, claims that he thought his girlfriend was a burglar when he shot her three times in the early hours of Valentine's Day 2013.
Mr Nel, working for the prosecution, has said that the only story that makes sense is that Pistorius shot at Reeva knowing it was her standing behind the door.
'That's not true,' is what the athlete replied with.
The prosecution have also picked up on several indiscrepencies in Pistorius's evidence - including his assertion that he ran onto the balcony to call for help, when police photos from the crime scene show that a duvet and a fan would be blocking his path.
Mr Nel also struggled to understand why Reeva would not respond to Pistorius when he was supposedly shouting at her to get down, and for the intruders he believed were in the bathroom to get out.
He also worked hard to get the athlete to admit that as he was approaching the toilet door her would be 'thinking and reasoning' and suggested that at that point would he not think the person in the bathroom could be Reeva.
Proceedings had to be stopped at one stage in today's hearing because Pistorius became emotional, and nearly had to be halted again because of claims that he was too tired.
Today was the 20th day of the murder trial, it will resume again on Monday at 8.30AM.