He challenged the Paralympic champion to explain the "improbability" of him running around his house with his gun still cocked in his hand as he shouted for help from the balcony and put on his prosthetic legs, as he suggested in his evidence. Pistorius started to cry as he told the prosecutor: "I wasn't thinking."
"You're not using your emotional state as an escape, are you?" Mr Nel asked him.
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In a day that was widely seen as the greatest challenge to the athlete's account since taking to the witness box last Monday, Pistorius broke down in tears several times, prompting the judge to call for two separate adjournments, or "tear breaks" as they have become known.
Barry Roux, his barrister, complained to Judge Thokozile Masipa that Mr Nel was deliberately going over sensitive ground already covered in an attempt to make his client cry and cause delays.
Mr Nel responded that he believed there was a "different view" as to why Pistorius was continuously breaking down. The judge rejected Mr Roux's complaint.
The athlete was asked what he shouted at the intruder. Pistorius paused, before shouting in a high-pitched voice: "Get the f*** out of my house! Get the f*** out of my house!"
South African chief state prosecutor Gerrie Nel gestures as he explains a possible scenario into how Oscar Pistorius might have fired on girlfriend Reeva Steenkamp. Photo / AP
The judge called an adjournment as the athlete burst into noisy sobs again.
After the break, Mr Nel suggested to Pistorius the reason why he had become emotional. "Isn't it because that's exactly what you shouted at Reeva?" he asked.
The 27-year-old athlete rejected the suggestion, saying: "By repeating those words, it reminded me of the night."
Mr Nel pressed Pistorius on whether he intended to shoot the suspected intruder. Pistorius has previously told the court that he was frightened, imagined that there was an intruder and armed himself to protect his own and his girlfriend's life.
He has also said that he fired "accidentally" after hearing a noise from behind the locked lavatory door.
"I was terrified. I didn't have time to think," Pistorius replied. "I thought someone was coming out to attack me."
"You fired at Reeva," Mr Nel told him. "That's not true," the athlete said weeping.
"Why are you getting emotional now?" Mr Nel asked him.
"I did not fire at Reeva!" Pistorius howled, prompting the judge to call another adjournment.
After the break, Mr Nel told Pistorius that he was relying on two different defences: "putative self-defence", that he fired at a perceived intruder intentionally, and "involuntary action", that he shot without intention as a reflex.
Mr Nel said that once again, Pistorius grew upset when he realised the "implications" of "getting your defences mixed up". The athlete denied the charge.
The case continues.