Where in the story does it state that the sage used the rinnegan to defeat the jubi?
The sage understood chakra before he even fought the jubi, his chakra control was probably absolute giving them the ability to use all the element releases without hand signs, like hohenheim.
With is powerful massive chakra reserves and wisdom he subdued the jubi and sealed it within himself.
None of these things were said in the story either! god damn son!
I believe that with the rinnegan he obtained the knowledge to understand chakra and then eventually produce jutsu. As with the rinnegan you can see chakra, it's much more believable that some one could obtain knowledge of chakra if they could actually
see it in the first place.
But here's also something to support your opinion,
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It doesn't say that he used the rinnegan to obtain that knowledge so either one of us could be correct here.
But I still think it's more believable that he had the rinnegan at birth and then founded jutsu later on in life as he realised his ab-normal powers.