This trick is easy to do and with some luck, you will not get hit at all in the entire battle. When the Sa-X sacrifices itself, get the Ice Beam. Then, when you start shooting the Boss in the chest, rapidly press B to keep hitting it. The Omega Metroid should cry in pain several times and will not be able to hit you.
In the battle with the Omega Metroid, when it swipes you, Samus will become motionless for a few seconds. However, if you rapidly press Up, you will cut this time down dramatically.