Double-amputee Pistorius, who ran the first leg of Thursday's heats as South Africa recorded a national record of two minutes 59.21 seconds, revealed on Friday morning he would not be running in the final.
The 24-year-old wrote on Twitter: "Haven't been included in the final for the SA Mens 4x400m. Pretty Guttered (sic). Receiving a lot of questions I don't know the answers too. Have the 2nd fastest time in SA and ran a 45.3 this week.
"Was team management's choice. I wish my team-mates all the best tonight, they all great sprinters and I hope they able to get on the podium!"
That wish at least came true, with Van Zyl running the anchor leg as South Africa claimed silver behind the United States in 2mins 59.87secs. Jamaica took bronze.
"We had the agreement before the first round that the slowest guy in the heats on the splits is not going to run the final and I'm going to take his place," said Van Zyl, who won bronze in the 400m hurdles on Thursday evening.
"I've always run the last leg for the last six years. Unfortunately Oscar's split was a 46.2 and he was the unlucky one who had to sit out.
"He's also going to get a medal and I think he's going to be very, very happy. He's only allowed to run the first leg in the relay and he's not the fastest guy out of the blocks. It was a decision by the management and everyone in the team was happy."