The result means South Africa go into the third and final Test at Lord's on August 16 with a 1-0 lead, with England needing to win to prevent South Africa from taking over their number one place in the Test rankings.
South African captain Graeme Smith, though, said neither side would take a significant edge into the deciding Test, insisting that there were "positives on both sides".
His England counterpart Andrew Strauss said he was happy with the strategy of playing four seam bowlers and leaving out Graeme Swann, although he admitted they "probably missed" the off-spinner in the second half of the game.
"With the weather forecast we thought our best way of winning was to win the toss and bowl first. We probably misjudged the wicket a little bit, it didn't do as much as we would have liked," he added.
Speaking separately, man-of-the-match Pietersen dropped a bombshell by saying he might not play for England again after the final Test but Strauss said "We want to win this Test match and we want as few distractions as possible.
"We've got a great chance of winning."
South Africa-born Pietersen followed up a thrilling century in the first innings by taking the first three wickets with his occasional off-spin bowling, despite never having taken more than one wicket in an innings in 87 previous Test matches.
Broad then took five wickets in 37 balls before South Africa declared at 258 for nine, leaving England an improbable 253 to win in 39 overs. They made 130 for four before the players agreed to a draw with six overs remaining.
England opened the batting with Pietersen, who hit 149 in the first innings, and the star of the match hit three fours in the first over from Morne Morkel.
But he was caught at mid-on on 12 when he mistimed a drive against Vernon Philander without scoring any further runs.
Alastair Cook and Andrew Strauss tried to keep the scoring rate close to the required rate of almost six-and-a-half runs an over.
But the chase ended after Strauss hit a full toss straight back to off-spinner JP Duminy while on 22, Cook fell to Dale Steyn four short of his half-century and Matt Prior was run out for seven.
Jonathan Trott and Ian Bell batted together for an hour before the players shook hands shortly after 7:30 pm (1730 GMT).
Smith said Pietersen's first innings had brought England back into the match after South Africa had done well to score 419 after being sent in -- and a crucial factor had been the amount of play lost because of rain.
"After lunch we came out and scored at a good rate. We wanted to be positive. We decided at tea we were going to go out and bowl and try to win. We were probably one wicket away from having a real go with 15 overs to go," he added.
An entertaining final afternoon did not seem likely on a rain-hit morning as Jacques Rudolph -- opening the batting in place of the injured Alviro Petersen -- and Graeme Smith progressed serenely to an opening partnership of 120.
Play was twice interrupted by rain and only 21 overs were bowled, despite lunch being delayed by half an hour.
Pietersen struck with his second ball, trapping Rudolph lbw in the last over before lunch -- the second time in the match Pietersen had dismissed Rudolph with his second ball -- and followed up in his second over after lunch with Smith's wicket.
It was the start of a hectic afternoon in which 116 runs were scored for six wickets in 27 overs.
England quick Stuart Broad finished with five for 69, with all his wickets taken for 29 runs in 37 balls.