The 17-year-old Northern Transvaal all-rounder made a defiant 90 in four hours and then removed the openers Marcus Trescothick and Anthony McGrath as England reached their target of 85 to win with seven wickets in hand.
The South African bowlers consistently pitched short and the England batsmen took up the challenge, with 62 runs coming in boundaries as they won with 25.1 overs to spare.
An earlier finish had seemed likely when South Africa resumed 66 behind and lost two wickets in four balls from Alex Tudor while adding only seven runs. When Bruce Stigant was bowled by Alex Morris South Africa were still 14 short of avoiding an innings defeat.
But Joubert, who hit 13 fours and a six from 175 balls, enabled them to squeeze 98 runs from the last three wickets, including a partnership of 81 with Malan Morkel. England needed a new ball burst from Andrew Flintoff to dismiss South Africa for 280. Joubert was leg before to Flintoff, who finished off the innings with 3 for 16 in 8.1 overs.