Boucher had joined Kallis with the score at a precarious 127-5 after Andrew Strauss had inserted the hosts and the two experienced batsmen calmly advanced the score to 216, before Stuart Broad finally trapped Boucher LBW.
The sixth wicket gave England a glimpse of the tail as the promoted Dale Steyn made his way to the crease but the WorldÃ¢â‚¬â„¢s no.1 rated fast bowler proved himself more than capable with the bat, comfortably nudging his way to a 57 ball 26 not out when bad light stopped play, just 3.2 overs after England had taken the new ball.
Earlier in the day, the tourists had continued their form from Durban with the struggling Ashwell Prince edging a Jimmy Anderson away-swinger to Matt Prior in the first over of the match. Graeme Smith was then dropped by man of the hour Graeme Swann from Graham OnionsÃ¢â‚¬â„¢ first delivery and for a while it looked as if England would live to regret that mistake.
But with AndersonÃ¢â‚¬â„¢s first delivery after lunch, Smith felt for another away-swinger and was well caught by Prior. It left the tourists reeling at 51-3 with Amla also back in the hutch, having been plumb LBW to Onions just before the break.
De Villiers and Kallis briefly threatened to form a significant partnership but the evidently relieved Swann had de Villiers caught at short mid-wicket by Strauss as he advanced down the pitch to the off-spinner. Swann then snared the out of form JP Duminy with his next delivery as the ball spun sharply from middle and off and caught a thin edge through to Prior.
Daryl Harper had earlier turned down two huge England appeals for similarly faint edges, one of which had produced an unsuccessful referral, but this time he was in no doubt, sending the left-hander on his way for a second consecutive golden duck.
Kallis however stood firm, reaching a typically stylish century, his 33rd in Tests, from 173 balls. As the Kookaburra ball grew soft and the sun burned away the thick cloud which had earlier disguised Table Mountain from view, batting became a much easier task, particularly for someone as technically astute as the 34 year-old all-rounder.
Onions briefly threatened with some uncomfortable tennis ball bounce and there was a hint of reverse swing for Broad and Anderson but Kallis, playing the ball late and swaying inside the line with a flexibility which defies his stocky build, was more than a match for them.
Neither Captain will be completely satisfied with a largely even dayÃ¢â‚¬â„¢s play but Strauss can find little to fault in the efforts of his attack. Each bowled with rhythm and the England skipper was able to distribute the overÃ¢â‚¬â„¢s evenly amongst them.
Smith meanwhile can once again think himself grateful for the brilliance of Kallis but the lack of contributions from Amla, Duminy, and Prince allows England to retain the psychological edge in the series.
If England can restrict the Proteas to 350 tomorrow morning they have every reason to feel confident that, on a pitch which should continue to assist the batsmen for the majority of the next two days, their top six can once again establish a position of authority in the match.
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BIOGRAPHY: Marcus Rashford