Bafana Bafana's returning coach, Brazilian supremo Carlos Alberto Parreira, expressed satisfaction that his team had not added to a record of eight losses in nine games, but admitted there was considerable room for improvement.
"This was a difficult match because Japan came here having scored a lot of goals recently. I'm satisfied with our performance while accepting that we will have to do much better," said Parreira, who coached Brazil to victory at USA 1994.
"Japan marked very well and that is why Benni McCarthy never got a clear-cut chance, but for my first match back in charge it was okay," added the coach, who quit last year to be with his ill wife in Rio de Janeiro.
It was also a new start for striker McCarthy, axed by Parreira's predecessor and fellow Brazilian Joel Santana, but the Japanese backline ensured there would be no comeback goals after eight months in the wilderness.
The Samurai Blue came closest to scoring through Makoto Hasebe and Shinji Okazaki in the first international staged at Nelson Mandela Bay Stadium, one of ten venues where the first FIFA World Cup finals in Africa will be staged.
Man-of-the match and South Africa goalkeeper Moeneeb Josephs foiled Hasebe, who plies his trade at German champions Wolfsburg, by tipping a fierce early drive over the bar before a near-capacity crowd.
Okazaki, a hat-trick hero when Japan crushed Togo 5-0 at home last month, then beat Josephs from an acute angle only to see his shot trickle wide beyond the far post.
And when the Kawashi Frontale custodian was called into action, he showed his prowess by getting down quickly and parrying a Siphiwe Tshabalala drive away for a corner.
Katlego Mphela, the only South African to score since a fourth-place finish at the 2009 FIFA Confederations Cup, had a chance as half-time loomed but fired wide.
The second half was even tighter with defences on top until 11 minutes from the final whistle when Josephs once again foiled Okazaki in what proved to be the game's final opportunity.
South Africa complete their friendly schedule for this year against non-FIFA World Cup qualifiers Jamaica on Tuesday 17 November in the central city of Bloemfontein.