Dejected England may now face a shake-up in terms of selection
England coach Peter Moores blamed his side's deficiencies with the bat after the visitors wrapped up the Test series with a five-wicket win at Edgbaston.
Moores admitted his side had been second best at the crease, with South Africa winning with a day to spare.
"We were playing catch-up cricket because we got 231 in the first innings," Moores told BBC Sport.
"If you score under 600 runs in a Test match, you're always going to be under pressure if the opposition play well."
After adding just 66 to their overnight score, with Paul Collingwood finishing on 135, England were dismissed for 363 to set South Africa a victory target of 281.
It had looked as though England were heading for an unlikely win when a dominant middle session saw them reduce South Africa from 65-0 to 93-4.
But South Africa captain Graeme Smith's 154 not out led ensured next week's fourth Test at The Oval will be a dead rubber.
I think we've seen three seamers and a spinner do well in world cricket. It's always going to be a lively debate and one we'll make sure we have
England coach Peter Moores
Smith combined good fortune - he was twice fortunate to be spared by umpire Aleem Dar and should also have been run out - with exceptional concentration and skill to lead his team to their first series win in England since 1965 with a day to spare.
"In this Test we fought very hard to get ourselves in a position where we had something to defend [with our second innings], and I thought 280 was defendable," conceded Moores.
"But we didn't count for Graeme playing so well.
"He played beautifully, because I thought Monty bowled well at him and asked lots of questions. But he came up with the right answers and you've got to give him credit for that."
Moores pledged his full support for under-pressure captain Michael Vaughan but admitted that deciding whether to continue to select just four bowlers was a "conundrum".
"If we hadn't played Paul Collingwood we wouldn't have got the runs," he said.
"I think we've seen three seamers and a spinner do well in world cricket. It's always going to be a lively debate and one we'll make sure we have, and then pick what we think is the best team."
Vaughan himself admitted England had lost to a better side and paid tribute to Smith's match-winning innings.
"It's a huge blow," Vaughan told BBC Test Match Special.
"We saw a very special innings and over the series they've been better than us. We just haven't batted well enough as a unit.
"At 93-4 we were well in the game and thought the game was on our side. But Smith played a very, very controlled innings.
"It's as good a knock as I've had played against me in terms of the context of the series."
Andrew Flintoff and Monty Panesar looked dangerous with the ball and took two wickets apiece, while James Anderson claimed one from 13 overs.
But Collingwood and Kevin Pietersen (94) aside, no England batsmen scored more than 25 in the second innings and Vaughan acknowledged his side's batting has not been up to scratch for some time.
"We tried to throw everything at them, I thought we bowled reasonably well at times and did put them under a lot of pressure, especially when we got that flurry of wickets," he said.
"We batted on a decent wicket on the first day and only got 231.
I'd like to think it was my best knock for South Africa in terms of the meaning that comes with it
South Africa captain Graeme Smith
"The ball swung but we really should have got a few more than we did. That's been a real worry for a long time now so there are areas, and certainly the batting, that we've got to look at."
Meanwhile, Smith said his 16th Test century was one of the most satisfying innings of his career.
"England made us play really hard, they put us under pressure and we had to come up with something special which we did," he said.
"I think England made us fight for this one. We had to work hard at Headingley and show a lot of discipline there to go 1-0 up which is the key in trying to get it sewn up before the last one.
"I think if England had won this one The Oval would have been very difficult for us.
"I'd like to think it was my best knock for South Africa in terms of the meaning that comes with it.
"Obviously I have some individual knocks which mean a hell of a lot to me but in terms of the country and the team and what we have achieved I think it is right up there."