In what is Andrew Strauss’s 100th Test match and 50th as England skipper, James Anderson and Steven Finn each took three wickets as it was left to South Africa’s lower order to provide a resistance.
JP Duminy scored 61 with Vernon Philander unbeaten on 46, approaching his maiden Test half-century, as the pair frustrated the hosts in the final session of the day.
The big news before the match surrounded the omission of Kevin Pietersen with his ongoing feud with the ECB overshadowing England’s preparations for what is a crucial Test.
Strauss’s side must win the match to draw the series 1-1 and retain their status as the world’s top-ranked Test side with the Proteas set to usurp their hosts if they can avoid defeat.
England, who had dropped Pietersen, selected spinner Graeme Swann in place of Tim Bresnan, giving paceman Finn - who bowled first change - another chance on his home ground.
Graeme Smith – who was delighted to have won the toss at the start of the day - was first to go when Anderson came around the wicket to the left-hander for the first time.
The South Africa skipper stabbed at a delivery wide of the off-stump and was caught behind, but given out only after England had reviewed umpire Kumar Dharmasena's decision.
Fellow opener Alviro Petersen survived another England review but did not last long thereafter, gloving a full delivery from Finn down the leg side.
Hashim Amla, who was prolific in the first match of the series, was bowled three balls later by Finn through the gate as the ball cut back down the infamous Lord's slope and demolished his woodwork.
Undoubtedly the most controversial moment of the day was the dismissal of Kallis - second on the all-time list of Test century scorers - as he gave wicketkeeper Matt Prior his third catch with a deflection off his glove.
Umpire Dharmasena initially rejected the appeal, but England had the decision successfully overturned by third umpire Rod Tucker with replays leaving the incident inconclusive with the batsman’s glove seemingly detached from the bat handle at the point of contact. Kallis and South Africa were left to feel aggrieved.
The dangerous AB de Villiers was well caught by Alastair Cook at third slip after he nicked Anderson, pushing outside off stump. He had failed to add a run having survived an England review when they felt he was lbw to Anderson.
Left-handers Rudolph and Duminy were mostly untroubled during a promising partnership, even against the off-spin of Swann turning the ball away from them, though Rudolph might have been run out on 40 had Anderson's throw from midwicket to the non-striker's end been more accurate.
Rudolph eventually departed as Swann got a full delivery to zip through, taking a faint inside edge, and the batsman was bowled for 42 with Duminy the final wicket to fall in the day as he was caught behind off a fired up Anderson.
Philander was left with 46 to his name at the close of plays as bad light brought an abrupt end to the final session with three overs still to bowl, with Dale Steyn also at the crease on 21.
It was undoubtedly the hosts’ day at Lord’s, and just the response that Strauss and his players needed after a troubling week for English cricket.