Rudolph was out for 25 on the first day of the third and final Test after edging a delivery from leg spinner Shane Warne to first slip. Hayden dived forward to take the catch.
Television replays suggested the ball bounced just before Hayden closed his hand around it.
''It's a tough one, we can only go on the evidence we saw on TV and you can't really say,'' said Kallis, leading South Africa in the absence of Graeme Smith who has a finger injury.
''You have to take Hayden's word on it,'' he told reporters.
''Jacques felt it was tight but it's difficult for him to say because it went fast. You tend to take the fielder's word on it, Hayden's not the type to cheat.'' Australian wicketkeeper Adam Gilchrist stood by Hayden.
''I thought Matthew Hayden got it, my gut feel was that it was there,'' said Gilchrist.
''Our stance has always been to leave it as a players' decision but the rest of world cricket has turned that down.'' With Australia leading the series 2-0, South Africa were on 238 for six when bad light ended play 11 overs early.