Gough was struck on the index finger of his right hand and had to ask for treatment on the field several times. Although in obvious pain, he batted on to help England amass a formidable total of 462 all out.
England's coach, David Lloyd, described the loss of Gough in conditions that promised to be ideally suited to his ability to swing the ball as "a massive blow", but he defended the last-wicket pair over their decision to stay on the field despite being offered the light moments before Gough's injury.
"There was no hint of it being too dark to see and the ball that hit him may well have done so even in bright sunlight," he said. "In the position we were in we were looking to stay on and score as many runs as possible. It was always the plan to bat two days if we could and the tail-enders were having a bit of fun out there.
"Maybe had it been the South African opening pair out there they might have gone off but it was never a consideration for us."
Lloyd expressed his sympathy for the Yorkshire player, who missed England's winter tour of the West Indies because of hamstring trouble after being dogged by injuries throughout his career.
"It is a cruel game," he said. "But he is a bouncy character and he'll be back. In the meantime, the onus is on the other bowlers, who will have to rise to the challenge and do the job without him."
Gough described the injury as a "bitter disappointment" in his comeback Test after a nine-month lay-off.
"It is enormously frustrating both personally and for the team as we are in a good position but I am confident the rest of the lads can help us take advantage of a promising situation," the Yorkshireman said. "One thing is for sure, I will be coming back, after all I have had plenty of practice at it."
England's new captain, Alec Stewart, added: "It is tough luck on Darren and the team but luckily we have still got enough top quality bowlers to do the job required."
Gough's injury apart, Lloyd was delighted with England's performance over the first two days.
"If you look at the facts it has been a tremendous performance for us. To be put in on a pitch where the ball is moving sideways and end up with 462 is just terrific.
"It puts us in a great position. I'm not saying we cannot be beaten but I'm absolutely delighted to have 462 on the board."
South Africa's coach, Bob Woolmer, felt his side had bowled much better yesterday than on the opening day, when England lost only one wicket.
"Nine wickets for 213 is more like par for the course in conditions such as these where the ball has swung and seamed but obviously we are not happy to concede 462 after putting the opposition in," he said.
"The ball swung a lot on the first day, which made it difficult to bowl. But having said that we should have done a lot better. We talked about it last night but the bowlers knew what they had to do and today was a different story."