The Leicester Tigers scrum-half scored early in the second half with a dart from an attacking lineout reminiscent of his first senior score at Bath in the EDF Energy Cup back in October.
Full-back Tom Homer kicked England into a 9-0 lead but they were hauled back in by the South Africans until Youngs scored to create a 16-11 advantage.
With Tigers wing Jack Cobden joining the action during the second half, forwards James Gaskell and Courtney Lawes scored further tries and centre Henry Trinder added a fourth in the final minute.
England will face New Zealand in the final after the Kiwis secured a 31-17 win over Australia in the other semi-final.
England Under-20 (vs South Africa Under 20)
15 Tom Homer (London Irish)
14 George Lowe (Harlequins)
13 Henry Trinder (Gloucester Rugby)
12 Luke Eves (Bristol Rugby)
11 Charlie Sharples (Gloucester Rugby) rep Jack Cobden (Leicester Tigers) 59min
10 Rory Clegg (Newcastle Falcons)
9 Ben Youngs (Leicester Tigers)
1 Ben Moon (Exeter Chiefs)
2 James Clark (London Irish) rep Jamie George (Saracens) 33min
3 Bob Baker (London Wasps) rep Shaun Knight (Gloucester Rugby) 56min
4 Graham Kitchener (Worcester Warriors)
5 James Gaskell (Sale Sharks)
6 Courtney Lawes (Northampton Saints)
7 Calum Clark (Leeds Carnegie, captain)
8 Carl Fearns (Sale Sharks)
Replacements not used
18 Dan Williams (Gloucester Rugby)
19 Josh Ovens (Bath Rugby)
20 Dave Lewis (Gloucester Rugby)
21 Rob Miller (Newcastle Falcons)
Scorers - Tries: Youngs, Gaskell, Lawes, Trinder; Cons: Homer 4; Pens: Homer 4.
South Africa U20: Francois Brummer; Gerhard van den Heever, Nicolaas Hanekom, Robert Ebersohn (capt), Sampie Mastriet; Lionel Cronje, Ross Cronje; Morne Mellet, Kyle Cooper, Coenraad Oosthuizen, Jan Andre Marais, David Bulbring, Marnus Schoeman, Rynhardt Elstadt, Christiaan Stander
Replacements: Zane Botha for Cooper 59, Caylib Oosthuizen for Mellet 65, Kenechukwu Ofakor for Marais 56, Yaasir Hartzenberg for Stander 71-77, Johan Sadie for Hanekom 74. Not used: Julian Redelinghuys, Rudy Paige
Sent off - Elstadt 64
Scorers - Tries: Stander, Hanekom; Con: Brummer; Pens: Brummer 3
