Scrum-half Youngs scored twice in the second half after England recovered from going a devastating start by the Springboks to set up an enthralling contest after half-time.
Flood had claimed England’s opening score as the tourists and added the rest of the afternoon’s points with the boot.
England struggled to gain any possession early on when tries by flanker Willem Alberts and hooker Bismarck Du Plessis gave the Springboks a 12-0 lead inside eight minutes.
Flood kicked a penalty to get England off the mark after a promising break from full-back Ben Foden, but the Springboks came straight back with a Morne Steyn kick and a converted try from scrum-half Francois Hougaard to stretch the lead to 22-3 by the 20-minute mark.
Youngs created the opening for the first England try, taking a tap penalty 35 metres out and enjoying the support of right wing Chris Ashton who passed on for Flood to score to the left of the posts, ducking and spinning out of the attempted tackle by Bryan Habana to dot down. Flood added the extras as England cut the deficit to 22-10.
Steyn provided a quick reply with a drop goal, and Flood then had to show his defensive mettle, making a last-gasp tackle on Jean de Villiers with the tryline beckoning.
The Springboks ended the half with a 15-point lead at 25-10 and Steyn kicked the opening points of the second period after England were penalised virtually under the posts.
Tigers No8 Waldrom earned his first taste of international rugby as a 47th-minute replacement for Ben Morgan to take the Leicester representation up to six in the white shirts.
The back-rower went close with an immediate break around the front of a lineout, but club colleague Youngs bettered that just seconds later, grasping the ball at the back of a Boks lineout and diving over.
The scrum-half was hit hard and high by Alberts, and made to wait by referee Rolland who went to the TMO before signalling the try. Flood added the conversion to cut the Boks lead to 28-17.
Steyn added another kick, but England were not ready to give in as Chris Robshaw claimed lineout possession and a huge drive from the pack took the tourists up to the line and Youngs darted over for his second try. Flood added the kick as England trailed by just seven points with almost 20 minutes to play.
A big England scrum then gave Flood the opportunity to chip further into the Boks lead, and he landed the penalty to make the score 31-27.
England, though, were put back under pressure when Waldrom knocked on from the restart and the hosts won a penalty at a reset scrum wide on the right. Steyn, who had missed two straight-forward kicks earlier, made it an unwanted treble as he pulled the kick wide.
But the home crowd celebrated again when JP Pietersen made a strong break on halfway and, when ball was controlled, he was back in position to dive in on the right to make it 36-27 and move the hosts more than one score clear again.