Obviously the three match final series at the end of a lengthy triangular series "matters" far more than the matches that come beforehand, as they are must-win fixtures. Similarly, the knockout games in a WC "matter" far more than the group games at the start. Australia for nearly a decade have been virtually impossible to beat in the important ODIs, even though they gave up games fairly regularly at other points. That's why they've been the dominant ODI team, and South Africa weren't. Compare their records in the must-win games and you'll see the trend.
By the way, I'm not suggesting for a second that Australia didn't care about the earlier games in those series at all. Any international team goes out to win every game they play. It's more that at big moments, Australia generally came through better, and they had clutch players like the Waugh's, Warne and Bevan who could snap a poor form streak to win a game at a crucial time. The '99 WC is the best example you'll see of this, though the 97/98 series works too. In the end, it doesn't really matter too much what happens at other times, any more than it matters that England were competitive for large parts of three test matches in the recent Ashes series. What matters is the end result, when you're determining who the better side is.