Skipper Wilkinson and his team briefly threatened a monumental upset as they stole a 19-17 interval advantage through Dan Scarbrough's interception try and 14 points from Wilkinson.
The Newcastle fly-half was restricted to just three further points after the break and South Africa cut loose to finish with eight tries and an aggregate total of 113 points and 15 touchdowns over the two games.
England head coach Brian Ashton has arguably learnt little in terms of the bigger World Cup picture, but Wilkinson has no regrets about being part of the trip.
He said: "I cannot speak any more positively about the spirit in this squad.
"It was always going to be a tough tour, but we have learned so much from this trip, probably more than the South Africans.
"It has been a joy to be on this tour. Everyone has been so positive, and I have been proud to captain them.
"The effort has been unquestionable, and this is why I got involved in rugby. Without this trip, we may not have known exactly what we had to work on or the players who could make an impact.
"I enjoyed the physicality of both games."
England were ultimately blown away by the sheer power of South Africa's forward game, conceding 38 points after the break, although it was a far better performance than they produced seven days ago.
Wilkinson added: "I thought we were in good shape at half-time, but too many mistakes cost us dearly in the second half.
"The desire and energy was massive, but the cumulative effect of a couple of rash decisions and some mistakes puts you in the wrong areas of the field.
"It was really up to us to shape the second half, but we were soon back to square one and the energy levels dropped off.
"The South Africans are excellent at capitalising on errors. Half a mistake, and they are away."
Head coach Ashton said: "We were never under any illusions about what we were facing when we came over here, and South Africa proved us correct.
"The priority was to identify players who could be part of the World Cup warm-up squad and perhaps the World Cup, but who don't usually figure in international squads.
"In that sense, it has been worthwhile.
"I was more than hopeful at half-time because we defended exceptionally well, and I thought if we could get more ball at the start of the second half we could be on the front foot and put our stamp on it.
"But they came out at a hell of a lick and then they cranked up their game for the last 20 minutes and you could see their energy levels were higher than ours."