Physical attacks will cause Omniscient to cast Return, resetting the battle. The player can prevent him from casting anything by attacking him with a weapon enchanted with Silence. When Omniscient is defeated, he casts Flare as a final attack.
An efficient method to defeat Omniscient is to summonCarbuncle, so Omniscient's spells are reflected back at him. Another method is to cast Berserk on him and then summon Golem. This way, he cannot use Return to restart the battle, and the party will not suffer damage from his physical attacks. Provided the party is under Reflect, or Omniscient is berserked or silenced, Omniscient's final attack should not pose a threat.
Another strategy is to use two Mystic Knights, one equipped with Blue Magic and other with Summon and use Spellblade Mute constantly, or one Mystic Knight can attack with Mute while the other will use Aeroga or summon Syldra. He is also susceptible to Magic Hammer; if he does not have enough MP at the end of the fight, he will be unable to cast Flare.
A simple method is to give both characters Reflect Rings. The player can then use magic. The Magic Lamp is helpful when low on MP.