England struck twice after lunch, removing Hashim Amla and Dean Elgar to have South Africa 172-3 at tea on the first day of the third Test here today.
Spinner Moeen Ali dismissed Elgar for 46, and pacer Steven Finn got Amla three overs later for 40 to give England a hint of ascendancy at the Wanderers as the tourists chase a first series win over South Africa in more than a decade.
England lead the four-game contest 1-0.
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De Villiers was unbeaten on 29 after cracking four fours in an attacking start to his innings.
Ali, Finn and Ben Stokes all had one wicket for England, with Stokes removing Elgar's opening partner Stiaan van Zyl for 21 before lunch.
South Africa, under new captain De Villiers after Amla quit as skipper following the second Test, won the toss and are chasing a way back into the series.
Amla was coming off a double century in the drawn second Test in Cape Town and, relieved of the pressures of captaincy, was in free-flowing form with seven fours. De Villiers began in attacking style, taking one delivery to get his range before hitting Ali for back-to-back boundaries.
But when Amla fell in a menacing spell from Finn for England's third wicket, South Africa were pushed onto the back foot. Du Plessis was 6 not out with De Villiers.
England picked an unchanged team from the second test. Offspinner Ali was retained on what's traditionally a fast bowler-friendly pitch.
South Africa went for an all-pace attack, calling up fast bowler Hardus Viljoen for his test debut and dropping spinner Dane Piedt.
South Africa were also forced into a dramatic late change today morning after wicketkeeper Quinton de Kock was ruled out with a sprained right knee after falling over at his home. South Africa had to call up Dane Vilas, who was put on a flight from the southern city of Port Elizabeth up to Johannesburg on the opening morning of the test and rushed into the team.
Pakistan were now 51 for two.
They had moved on to 76 for two at lunch but Azhar Ali had failed to add to his interval score of seven not out when he was literally knocked off his feet by a Ball yorker and given out lbw by Dharmasena.
The batsman reviewed and Ball, presented with his England cap before play by his uncle Bruce French, the former England wicket-keeper, had a nervous wait for his first Test wicket.
But this time, thanks to a tight 'umpire's call' verdict showing the ball clipping leg stump, technology worked in Ball's favour.
Pakistan were now 77 for three but veterans Younis and Misbah, as they had done so often before, steadied the innings.
Their cause was helped when Misbah was dropped on 16 by Joe Root, who grassed a tough slip chance off fast bowler Steven Finn.
Younis struck several elegant drives in his innings but he gave his wicket away on 33 when he clipped Broad straight to Moeen Ali at square leg to end a stand of 57 with Misbah that had had taken Pakistan to 134 for four.
Misbah, playing in his first Test at Lord's at the advanced age if 42, was not in control of a gloved hook off Broad but looked much better in forcing him through point for four.
Earlier, as expected, left-arm quick Amir was selected for his first Test appearance since the infamous 'spot-fixing' clash against England at Lord's in 2010.
That match saw Amir and Pakistan new-ball partner Mohammad Asif deliberately bowl no-balls on the instructions of then captain Salman Butt as part of a newspaper 'sting' operation.
All three received five-year bans from cricket and jail terms.