The trouble comes from Preta Path who can probably still suck her mana, Animal Path who can flood the field with summons, and the Path that can reanimate the other paths (forgot the name).

This is the point everybody here forgets.

Everyone talks about speed or that Pain can't hit Saber because she has that "anti-magic shell", but if we go for this, then Saber likewise can't do shit to Pain because he will simply dodge everything. Speed levels in Naruto are higher than anything Saber can do.

So, Round 1 would be Pains win. Pain would just sit out the fight, dodging Sabers attacks and sucks that mana out until she drops.

Round 2 would be more interesting. Saber could heal herself with Avalon but she still couldn't hit Pain I'd say. She would need to somehow wreck every single path or atleast knockout the Preta Path. Since the Rinnegan on 6 paths will most likely see any attempt of Saber to hit the Preta Path, Pain would once again just dodge everything she has. If she goes for that one-shot-try, I wouldn't know. Is an all-out Avalon attack stronger than the absorb of Preta? Nobody knows.

Round 3 would be almost identical to Round 2 to be honest. I can't see Saber taking anything against Pain. People vastly overestimate or underestimate the speed of Naruto characters. She still wouldn't be able to hit the "main" pain. And any attempt of hitting a Path would only end up in another Path doing something to counteract her attacks. But she might have a chance if she takes out the Naraka path first.

Bloodmatch Round

Well, considering Nagato not being at his strongest as the Pain in the "Pain Arc" and beating Saber every time in my opinion, him at full strength - edo tensei'd - would wreck Saber even harder.