Andrew Strauss described South Africa's actions in the ball-tampering row as "malicious" after England battled to a draw in the third Test in Cape Town.
South Africa accused Stuart Broad and James Anderson of tampering on day three but did not officially complain.
England skipper Strauss said: "We're not particularly happy about it, and I strongly refute those allegations.
"If you make allegations, you've got to be very clear or confident about what the other team were doing."
The dispute continued to cast a shadow over the match, despite England's tenacious display ensuring the series - with one Test to play - cannot be lost by them.
South Africa were angered on Tuesday by television footage showing Broad stepping on the ball with his spikes, while there were also claims Anderson picked at the ball.
But Strauss said: "I do think that the South Africans announcing it to the media, without being totally clear in their minds whether they were going to put in a formal complaint, is a little bit malicious.
"I really don't feel there was any concerted effort on anybody's part to alter the state of the ball.
"I appreciate that some of that footage didn't look amazingly good. If the spotlight is on [us], we've got to be very careful that we are beyond suspicion.
"Towards the back end of a series, emotions start running a little bit high. That's understandable. I hope today has gone some way to making sure the game of cricket is the main story."
Smith deflated after last-ball thriller
England team director Andy Flower backed up his captain in refuting any claims of ball tampering but admitted Anderson had been "naive".
"Jimmy was shining the ball and when he turned it over it was almost as if he was absent-mindedly assessing the rough side," he told BBC Radio 5 live.
"He then picked at a loose piece of leather which he shouldn't have done. He should have taken it to the umpire and they would have cut it off with a pair of clippers.
"But there was certainly no malicious intent there. I'd be surprised if any impartial observer said that Jimmy was scratching at that rough side.
"If anything, he's guilty of naivety. To stand there and put your fingers anywhere near the rough side is naive because the cameras are following you all the time.
"It does look bad but he was doing nothing to alter the condition of the ball. We will certainly make sure none of the guys are that naive again."
South Africa captain Graeme Smith admitted he hoped the two teams could put their differences behind them when the final Test concludes.
"The series is competitive and is being played in a hard way, but I have no doubt that when it is finished there will be a beer shared," he said.
"That's the way cricket is played, and it's the way I like my team to play the game. I don't see any off-field tensions.
"It's pretty tough on the field, and that's the way people want to have it."
Former England batsman Geoffrey Boycott told BBC Radio 5 live that the whole issue had been blown out of proportion.
"These days you can't do anything on a cricket field," he said.
"I think there were 30 cameras at the match so you can't even pick your nose because they'd pick it up.
"A player would be stupid to do anything wrong to the ball. There is a law where the umpires often, and at irregular intervals, check the ball and they saw nothing wrong with it.
"If you look at the clip then Jimmy Anderson could well just be picking something off the ball. Technically, if you were getting rid of a bit of grass or something then you should show the umpire first.
"But I don't think there was anything in it and I think the South Africans made too much of it. I thought they were trying to get their excuses in early in case they lost."
Strauss also paid tribute to Ian Bell after his dogged innings helped England earn their dramatic draw at Newlands.
Bell, who was under pressure going into the match, struck 78 from 213 balls as England survived a tense finale.
"I know how desperate Ian has been to play an innings like that for us," said Strauss, with England 1-0 up with one Test remaining in the four-Test series.
"He showed his class and he's entitled to feel pretty satisfied right now."
England began the day on 132-3 and looked to be heading towards defeat when nightwatchman Anderson and Jonathan Trott were out in the morning session.
But Paul Collingwood dug in to score a painstaking 40 from 188 balls, and he and Bell batted together for 57 overs in a stunning rearguard action.
Bell was out with 17 balls left in the day, but last pair Graeme Swann and Graham Onions clung on.
England saved the first Test in similar circumstances at Centurion, and Strauss admitted: "It wasn't any fun the first time and it didn't get any better today.
"We started the day as outsiders and we knew it would take something pretty special to avoid defeat, but we got that as Paul and Ian played two exceptional innings.
"Just when we thought they had got us there, South Africa came back and you have to congratulate them for a brilliant effort today.
"But Graham Onions - he's a legend, isn't he? We're very thankful to still be 1-0 up in the series."
Bell revealed his satisfaction at finally playing a big innings for his country when they most needed it.
"It's something I knew I had to do - get ugly runs when it counts most," said the Warwickshire batsman.
"I couldn't have wished for a better partner than Paul in trying to do that. I've done it for Warwicks before, but not England, and it was great to do it and for us to get over the line.
"This is fantastic momentum for us to go to Johannesburg with."
Collingwood, who was out with 13 overs left in the day, admitted he was finding the tension much easier to cope with while he was out in the middle.
"They're great when you're out there, days like this, but in the changing-room it's just horrible," he said.
"That was a huge result for us. We've done pretty well today because the odds were hugely against us, what with the position we were in and the way they were bowling.
"We were under an awful lot of pressure, but we've got every right to celebrate that today and we want to go on and win the series now."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.