Pokemon Sapphire Version

I would recommend using Magneton to weaken, paralyze, and defend with Rayquaza. If Magneton does not know Thunder Wave, then use the Move Tutor at the west edge of Fallarbor town to teach the move to it. Magneton, being an Electric and Steel type, is resistant to all of Rayquaza's attacks. Maybe try to raise it up in level a bit if that doesn't work. Also, use a weak Electric attack to start damaging Rayquaza, but then use other types of attacks after it cannot use Outrage anymore to whittle its health down as close to nothing as possible. Rayquaza's Rest move has 15PP, Outrage has 5, I think, so once those moves are out of PP whittle its health down as close as possible. Take along a bunch of Revives if you need to.