The Sage never had the Rinnegan to begin with! He had normal eyes...
During his time even though chakra and "jutsu" existed their exact mechanism of working and relation was unknown. Ninjutsu was like "magic" and it was something that could be performed by chance.
However there were some few individuals who could intuitively control chakra. The Sage was among these lucky one.

When the Juubi plagued the world it was onto people like the Sage to protect others. Obviously they all failed-with the exception of the Sage! Not only the Sage was a genius, he also had something that set him apart from others like him! A Kekki Genkai! Wood release!

The Sage knew that it would be impossible for him to defeat the Juubi head on.
So instead he developed a sealing jutsu and with help of his Wood Release managed to temporarily subdue the Juubi, giving him enough time to perform his sealing technique and seal the Juubi inside himself! And so he became the first Jinchuriki!

EDIT: Add the possibility that the Sage was also a Sage(nature chakra user), him defeating the Juubi without any dojutsu becomes much more acceptable!!

However the Juubi's chakra was too strong and it began to affect his body!(Proof: Naruto's whisker marks are because of Kurama's chakra effect when Kushina was pregnant)
It caused his eyes to mutate into a Sharinnegan! (i.e the Juubi's eye)

With his new dojutsu the Sage was able to decipher the exact mechanism of of Ninjutsu!
Ninjutsu was no longer "magic"! The sage proved that anyone with proper training could perform this "magic" aka Ninjutsu and developed new techniques himself!! The Sage began teaching the world about his techniques along with his message of peace...
And so was the "Father of all Ninjutsu" aka the "Sage of the Six paths" born

The pattern behind the Sage's cloak.
Izanagi:
In Tob's words,
Tobi also said that Izanagi was based on an ability the Sage had: Creation of all Things(say complete Izanagi).
This would mean that this ability of Sage could be considered as the ultimate genjutsu(since they are related) ever- converting illusions into reality out of nothingness!!

From what we know the Rinnegan doesn't have the ability to cast genjutsu like the Sharingan!
Nagato never used any sort of genjutsu(at least none that I remember).Please remember that I am talking about Genjutsu specifically related to dojutsu like MS's Tsukuyomi
So how was it the Sage could perform the Ultimate Genjutsu if he had the same "eyes" as Nagato which are unable to cast even a basic genjutsu?!!
Now I am expecting a thoughtful reply not a lame one like "He was the most powerful shinobi ever"/"The Sage could do anything!!"....

Madara's Meteorite Attack:
Madara used Bansho Ten'in(Rinnegan ability) and Susanoo(MS ability) in conjunction to drop two large meteors!
Now both M.Sharingan and Rinnegan have mutually distinctive abilities!
And Madara could activate only Rinnegan or his EMS at a given moment
But Madara was able to use Susanoo while his Rinnegan was active! This shows fusion of both's abilities is possible!
If so, isn't it also possible for a fusion of both dojutsu? This gives credibility to the possible existence of such a dojutsu i.e Sharinnegan

(Although I don't remeber the exact wording nor chapter)
Itachi's quote to Nagato:
Itachi was saying that if both the powers of Rinnegan and Sharingan were used simultaneously one could do anything-reference to the Sage's godlike ability aka Creation of all Things(true form of Izanagi).

This one is more like a theory! So use your own logic to test its validity!
The reason why Tobi has one Rinnegan and one Sharingan


All this suggests that the Sage had powers of both, the Sharingan and the Rinnegan
Since it was a mutation caused because of the Juubi's chakra, Sage's dojutsu was passed on to his descendants.
And it was from Sage's original dojutsu that the Sharingan, byakugan etc originated.
And the Sage's dojutsu is the same as Juubi's eye aka Sharinnegan aka Rinnegan with 9 tomoe
Which is to say:
The Juubi's eye is the origin of all Dojutsus!!

The Sage used his Izanagi to split the Juubi into nine Bijuus so it's logical that you would need to use Izanagi to merge them into one as well!
Now the Sage was said to have cast "complete Izanagi"(no blindness) with his "eyes". So if Tobi really wants to revive the Juubi he also need to cast a "complete Izanagi".
Agreed?

We know that you require Senju dna + Uchiha sharingan to cast Izanagi. But in this case you lose your sharingan like Tobi and Danzo did.
We now know that sharingan can be progressed to rinnegan.
So this essentially means that the rinnegan has its roots in Uchiha dna.
So doesn't it mean that Nagato should have been able to cast "complete Izanagi" with rinnegan since he was an Uzumaki(Senju dna) and had rinnegan(Uchiha eye)?
If not Nagato at least Madara should be able to!
But we never saw Nagato use Izanagi nor Madara! It's likely they can't!

Tobi needs to cast a complete Izanagi to revive the Juubi! But how?
Tobi despised Danzo's Izanagi saying that it was incomplete. But was Tobi's Izanagi any better? He also lost his eye which means his' was also incomplete, at that time!
Now Tobi has both Sharingan and the Rinnegan implanted!
Both the Rinnegan and the Sharingan have mutually distinctive abilities!
This wouldn't be any different than before unless
Now if the Sage could cast a complete Izanagi with his "eyes" it should mean that he had power of both Sharingan and Rinnegan!
The Juubi's eye is a combination of both the Sharingan & Rinnegan.
So in a nutshell, the Sage got the Sharinnegan from the Juubi!

lol
I wasted so much time typing this...
Kishi already hinted this! See chapter 510 pg11
We see the Sharinnegan! That time I only thought that it was a reference to the Juubi and not the Sage's dojutsu!