In reply of South Africa’s first-innings 309, England were tottering at 54-4 when Bairstow (72 not out) launched a strong recovery alongside Ian Bell (58) and shared 124-run stand for the fifth-wicket to guide the hosts 208-5 at stumps.
Bairstow, playing only because England segregated Pietersen over his text-messages to South African players about skipper Andrew Strauss and Coach Andy Flower, demonstrated skill and maturity and recorded his maiden Test fifty.
Bairstow, whose so far 137-ball knock is studded with nine boundaries, will recommence the England bids to build a considerable lead alongside Matt Prior (22 not out) on Saturday.
Pace duo Morne Morkel and Dale Steyn were collectively responsible for the calamity of the England top-order with both bagging two wickets apiece.
Morkal triggered the collapse by uprooting the stumps of opener Strauss (20) on the stroke of lunch.
Steyn banged shortly into the interval and scalped Alastair Cook (7) and Jonathan Trott (8) in the successive overs leave England in deep trouble.
Morkal continued to sprinkle salt on England wounds and edged diminutive James Taylor (10) to skipper Graeme Smith early in his next spell.
Under the disastrous circumstances, Bairstow and Bell shouldered the responsibility and gained the momentum gradually. The two batsmen defied the South African pace and spin attack with levelheaded approach.
Seamer Vernon Philander eventually separated the pair by dismissing Bell, who fall prey to Alviro Petersen at mid-wicket.
In the morning session, Philander slammed a half-century to take South Africa past 300 after they resumed the day at 262-7.
Philander (61) shared crucial runs with Steyn (26) Morkel (25) before getting stumped off spinner Graeme Swann.
Steven Finn was the pick of England bowlers with the figures of 4-75. His fellow seamer James Anderson finished with 3-76.
England, who lost the opening Test at The Oval by an innings and 12 runs before drawing the second Test at Headingly, must win this Test to retain their World No.1 Test status.
England VS South Africa 3rde Test Scorecard