The tourists appeared to have it in their grasp to level the Royal London Series at 1-1, and set up a Lord’s decider on Monday, when they narrowed their chase to just 10 needed from as many balls.
But sixth-wicket pair David Miller (71no) and Chris Morris fell two runs short after opener Quinton de Kock (98) and De Villiers himself had worked hard too in response to 330-6 - a total in which England all-rounder Ben Stokes equalled his one-day international career-best of 101.
For good measure as De Villiers came to terms with his team’s near miss, he had to reflect too on his perception that umpires Chris Gaffaney and Rob Bailey considered - momentarily at least - South Africa might have somehow altered the condition of the ball.
After a winter in which South Africa Test captain Faf du Plessis was fined his match fee in similar circumstances against Australia in Hobart, in his case using saliva to shine it while sucking on a mint, any suggestion of ball-tampering is emotive.
De Villiers’ conclusion, after no action was taken in this case, is that a tacit acknowledgement of innocence has been made.
Even so, asked if he felt initially that he was being held responsible on this occasion, he said: “Yes, I did.”
The intervention came after 33 overs of England’s innings, but the officials did not decide to change the ball.
De Villiers added: “The umpires felt the condition of the ball changed, in a way making me feel we were responsible as a team.
“I was quite upset about that ... (but) it’s done and dusted now. Nothing happened, there were no fines given or anything like that.”
He made his feelings clear to the officials.
“I expressed I was quite upset about it,” he added. “I told the umpires we had nothing to do with the condition of the ball ... no further steps were taken ... and we move on.
“Generally there is a warning or a fine, but none of that happened. That tells me they realised we were innocent in this case.
“I honestly think it was just a bad ball today ... which happens sometimes, the leather comes off sometimes. Unfortunately, the umpires didn’t agree with that.”
Several hours later, it fell to England captain Eoin Morgan to reflect on a success which had become improbable but was closed out by fine death bowling from Jake Ball and then in the last over Mark Wood.
“We needed wickets - that’s what we talked about,” he said. “So we went for the more attacking option.”
Remarkably, no wickets came - but South Africa’s chase nonetheless fizzled out inadequately into singles.
“It’s unbelievable really,” added Morgan. “I don’t know how to explain it really. To have won it without taking wickets is an unbelievable effort.
“Woody’s yorkers are usually very good. So going against what he’s naturally good at, and just with his raw pace and variation with cross-seam off the wicket, worked through the day. Then in that last over I think he might have bluffed him a couple of times.”
De Villiers admitted he was beginning to believe his team should win.
“I got a bit excited there at the end - I thought we had it in the bag,” he said.
“I thought Chris and David played a great hand in that partnership to get us so close ... (but) you’ve got to give credit to the last two bowlers for England.
“They showed some great skill and good plans. Unfortunately it didn’t go our way. We didn’t get that lucky bounce ... little edge over the wicketkeeper.
“We were just waiting for one little break like that, and it would have been game over - but it didn’t come.”