The Springboks finished the year with 12 games, seven wins, three losses and two draws. They bowed twice against world champions New Zealand and once to Australia.
Saturday's win against England clinched the Boks' victorious tour of Europe following wins over Ireland (16-12) and Scotland (21-10).
The England match was especially important, since their last clash during the Roses' South African tour in June ended with a 14-14 draw in Port Elizabeth.
"I'm very happy with the first year. You always know it's going to be tough if you lost a lot of guys, but a reasonable start and I think we can only grow as a team from here," said Heyneke after the tour to Europe.
"We've lost three out of 12 and the great thing for me is we started at number four in the world and ended number two. There's a lot of better things we can do if we keep our feet on the ground."
Already 2013 looks like the year Meyer tackles the club rugby system that leave players too exhausted to play for the national team.
"We have to manage the players better, we have to look at the systems," he hinted.
Meyer had traveled with an inexperienced team after injuries forced him to leave many senior players home. The likes of wing Bryan Habana, the country's rugby player of the year, centre Pierre Spies, hooker Bismarck du Plessis and loose forwards Schalk Burger were not considered for the tour.
The season started with England's tour to South Africa in June, where the Boks won the first two and drew the last.
They were tied with Australia in second place after the Rugby Championship, where they lost against the side away but won at home, beat Argentina once and drew another, and lost twice against the Kiwis.
New Zealand ended the year firmly dominating the game, but the Springboks nevertheless had a good season.
The team drew criticism all the same, notably from respected commentator Naas Botha. Along with former South Africa and Italy coach Nick Mallet, Botha likened their playing style to "watching paint dry".
"We have the skills and players to play a similar brand of rugby to the All Blacks, if not better," said Botha.
"But one has to wonder if we have become so focused on dominating physically that we have lost all our creativity. I think this team is capable of much more."
Botha has said the team plays as a group of individuals, and pointed out their preference of kicking over playing running rugby.
"Why is the team's first option always to get rid of the ball?" he asked.
Others, like rugby columnist Archie Henderson, have bemoaned former Pretoria-based Bulls coach Meyer's fear of taking risks.
"The overwhelming impression ... is that Meyer is a coach lacking in enterprise," Henderson wrote recently.
"He is a coach whose fear of losing is greater than his sense of adventure."
But Meyer, a self-confessed "slow starter", said he was proud of the team's progress.
"There's a lot of youngsters under 21, babies when you picked them. After a long year and a really long tour, suddenly those guys have become men, the (Eben) Etzebeths of the world, and Marcel Coetzee and Pat Lambie," he said, naming a few young players who have excelled.
He's also played down the season's 58 percent win ratio.
"If you take the draws then it's 75 percent. Our best seasons, 2009 and 2007, we lost more than we lost this year."
"With a management team that started late, a lot of those guys were still in Super Rugby, the planning wasn't where it should be, and we've ended number two," Meyer added.
He has also avoided growing debate over his team selections, with a notable lack of black players. He picks "the best side", he says.
With the season now over the Boks can look forward to a carefree Christmas, and next year start preparing for the 2015 World Cup in England with Northern Hemisphere experience gleaned during their last tour.