Vaughan's early dismissal added to England's frustration after South Africa had batted for all but five minutes in the morning session to extend its first innings.
Kirsten led a batting recovery as the last three South Africa wickets added 200 runs.
Kirsten and Zondeki (59) equaled a record eighth-wicket partnership, and shared 150 runs in over three hours to wrest the initiative from England.
Resuming the day on 260 for seven after deciding to bat first, Kirsten and test rookie Zondeki frustrated England for another 51 minutes before swing bowler James Anderson separated the pair.
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