Jonathan Trott fell for a duck as the tourists were bowled out for 260 at Bloemfontein.
Trott had been the hero of the drawn first match with an unbeaten 211 but little went right after he won the toss and chose to bat first. He was at the crease sooner than he would have expected after Sam Robson and Alex Lees both fell early. And the 33-year-old lasted only four balls before turning a delivery from Chris Morris to leg slip as England slumped to 16-3.
Opener Lyth steadied the ship alongside James Vince, the pair adding 66, while Bairstow then joined fellow Yorkshireman Lyth to repair more of the damage.
But Lyth’s innings was ended at 65 by Stiaan van Zyl, and in the next over Bairstow was bowled by Kleinveldt for 47.
That left the tourists in trouble once again at 164-6, and they were grateful to another Yorkshire duo, Adil Rashid (68)and Liam Plunkett (24), for helping them reach 260. South Africa’s reply was 29-1.