Farrell has been plagued by injuries since switching codes 20 months ago and did not have a good day with the boot against the Springboks.
He missed both penalty attempts but World XV coach Dwyer said the Saracens centre can play a similar role as Will Greenwood for his country.
England have failed to find a suitable replacement for Greenwood following his retirement at the World Cup in 2003 and Dwyer said: "I think Andy will take to the number 12 position at the highest level easily.
"The more he plays there, the better he will be.
"He has got everything which is required of the position and I don't think he will have any problems there.
"He can play the same way that Will Greenwood played it.
"His presence outside Jonny Wilkinson was vital for England. There are some differences between them, but Andy can do a similar job.
"If I was coaching the team, I would want Andy Farrell or someone like him in that position."
Dwyer also backed Lawrence Dallaglio to play a key role for England in the coming months following the dismissal of head coach Andy Robinson.
Dwyer explained: "He is a terrific leader. I'm not saying bring him in as captain, but leadership is required in more people than the captain.
"I would have him in because he makes a big difference to the squad."
South Africa head coach Jake White declared himself satisfied with the final match of a tour which started with two defeats - and did not rule out returning to Leicester to coach Tigers after next year's World Cup.
Tigers' head coach Pat Howard leaves the club at the end of the season to help run his family's business in Australia and White has been earmarked as a possible successor.
White is believed to have already spoken to representatives from Tigers, and he said: "After the World Cup, you never know. It's been a great experience in Leicester."
White was delighted with the performance of his youngsters at the Walkers Stadium.
He added: "The most important thing is that a couple of youngsters got some game time and know what it's like to play against some very good players and win in a Springbok jersey.
"This group of players have not played much together, so it was a good win and to see the character they showed was exciting. I'm very happy with where we are.
"We have beaten every ranked team in the last three years and there aren't many teams that can say that."