It was just the start the tourists wanted after arriving without injured regular captain Graeme Smith.
South Africa captain Graeme Smith had made a late bid to regain the player's allegiance.
BBC: Craig Kieswetter is called into England's one-day squad
Skipper Graeme Smith steered the visitors, who lead the three-Test series 1-0, to 23-0 by the close.
Burke again threatened with a low curler that goalkeeper Graeme Smith did well to turn round the post.
Niall McGinn fired in with just 69 seconds played after Saints keeper Graeme Smith parried a long-range shot.
Martin returned to remove openers Graeme Smith and Herschelle Gibbs by the ninth over of South Africa's reply.
United Cricket Board chief executive Gerald Majola welcomed the squad home and offered his support to Simons and captain Graeme Smith.
Andrew McDonald took 3-25, while Mitchell Johnson ended the day on 3-37 and forced Graeme Smith to retire hurt.
Meanwhile, South Africa coach Mickey Arthur is confident that skipper Graeme Smith will regain form in the VB Series.
He shared an opening stand of 136 with Graeme Smith (65) and cracked four sixes in his run-a-ball 140.
The visitors were convinced South Africa captain Graeme Smith had been caught when on 15 during the first innings.
Zaheer Khan reduced the tourists to 6-2 in the seventh over when he dismissed Graeme Smith and Ashwell Prince.
Captain Graeme Smith (35no) steered the tourists, who lead the three-match series 1-0, to 46 for two at close.
Skipper Graeme Smith (hamstring), all-rounder Jacques Kallis (elbow) and opening batsman Hashim Amla (groin) are all expected to be fit.
Graeme Smith (0) and Hashim Amla (1) were out early as South Africa slumped to 2-2 before Jacques Kallis' arrival.
But Flintoff gave England hope after removing Graeme Smith (7) late on to leave South Africa at 38-1 at stumps.
This meant that he failed to detect a vital edge from Graeme Smith's bat when he had scored only 15.
Nikica Jelavic then ran on to a woeful back-pass from Richie Towell to round Graeme Smith and roll the ball home.
In the first Test against Pakistan in Dubai, Petersen scored 67 out of an opening partnership of 151 with Graeme Smith.
Paul Hartley fired the home side into the lead seconds before the half-time interval with an accurate half-volley past Graeme Smith.
South Africa captain Graeme Smith claimed the extra half hour with last-wicket pair Ravi Rampaul and Nelon Pascal at the crease.
Graeme Smith (11) edged behind shortly after to hand the seamer his third wicket and suddenly South Africa were on the rack.
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The side will again be led by Graeme Smith, who hit two double centuries in the drawn series in England in 2003.
"He is the player I respect most, " said Proteas captain Graeme Smith.
South Africa captain Graeme Smith admitted he hoped the two teams could put their differences behind them when the final Test concludes.
Lee Wallace created Hearts' only good chance of the first half when his left-foot strike tipped round the post by Graeme Smith.
Johan Botha will continue to captain the team in Graeme Smith's absence.
Andrew Flintoff's late dismissal of Graeme Smith will give England plenty of encouragement when South Africa resume their innings at 38-1 on Thursday.
Graeme Smith opted to bat first after winning the toss, with his side still smarting from their 1-0 defeat in the Test series.
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